1
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Romero-Rodríguez A, Ruíz-Villafán B, Sánchez S, Paredes-Sabja D. Is there a role for intestinal sporobiota in the antimicrobial resistance crisis? Microbiol Res 2024; 288:127870. [PMID: 39173554 DOI: 10.1016/j.micres.2024.127870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/24/2024]
Abstract
Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.
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Affiliation(s)
- A Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México 04510, Mexico.
| | - B Ruíz-Villafán
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - S Sánchez
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - D Paredes-Sabja
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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2
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Aleksandrova EV, Ma CX, Klepacki D, Alizadeh F, Vázquez-Laslop N, Liang JH, Polikanov YS, Mankin AS. Macrolones target bacterial ribosomes and DNA gyrase and can evade resistance mechanisms. Nat Chem Biol 2024:10.1038/s41589-024-01685-3. [PMID: 39039256 DOI: 10.1038/s41589-024-01685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/19/2024] [Indexed: 07/24/2024]
Abstract
Growing resistance toward ribosome-targeting macrolide antibiotics has limited their clinical utility and urged the search for superior compounds. Macrolones are synthetic macrolide derivatives with a quinolone side chain, structurally similar to DNA topoisomerase-targeting fluoroquinolones. While macrolones show enhanced activity, their modes of action have remained unknown. Here, we present the first structures of ribosome-bound macrolones, showing that the macrolide part occupies the macrolide-binding site in the ribosomal exit tunnel, whereas the quinolone moiety establishes new interactions with the tunnel. Macrolones efficiently inhibit both the ribosome and DNA topoisomerase in vitro. However, in the cell, they target either the ribosome or DNA gyrase or concurrently both of them. In contrast to macrolide or fluoroquinolone antibiotics alone, dual-targeting macrolones are less prone to select resistant bacteria carrying target-site mutations or to activate inducible macrolide resistance genes. Furthermore, because some macrolones engage Erm-modified ribosomes, they retain activity even against strains with constitutive erm resistance genes.
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Affiliation(s)
- Elena V Aleksandrova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Cong-Xuan Ma
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Faezeh Alizadeh
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jian-Hua Liang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA.
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3
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McLellan JL, Hanson KK. Differential effects of translation inhibitors on Plasmodium berghei liver stage parasites. Life Sci Alliance 2024; 7:e202302540. [PMID: 38575357 PMCID: PMC10994859 DOI: 10.26508/lsa.202302540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024] Open
Abstract
Increasing numbers of antimalarial compounds are being identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of the molecular target or mechanism. A deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential could prove useful. Here, we probed that relationship using the Plasmodium berghei-HepG2 liver stage infection model. After determining translation inhibition EC50s for five compounds, we tested them at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, followed by parasites to 120 h post-infection to assess antiplasmodial effects of the treatment. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to the release of hepatic merozoites for all compounds. We also demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy does not determine antiplasmodial efficacy for these compounds.
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Affiliation(s)
- James L McLellan
- https://ror.org/01kd65564 Department of Molecular Microbiology and Immunology and STCEID, University of Texas at San Antonio, San Antonio, TX, USA
| | - Kirsten K Hanson
- https://ror.org/01kd65564 Department of Molecular Microbiology and Immunology and STCEID, University of Texas at San Antonio, San Antonio, TX, USA
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4
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Lyu Z, Ling Y, van Hoof A, Ling J. Inactivation of the ribosome assembly factor RimP causes streptomycin resistance and impairs motility in Salmonella. Antimicrob Agents Chemother 2024:e0000224. [PMID: 38629858 DOI: 10.1128/aac.00002-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
The ribosome is the central hub for protein synthesis and the target of many antibiotics. Although the majority of ribosome-targeting antibiotics inhibit protein synthesis and are bacteriostatic, aminoglycosides promote protein mistranslation and are bactericidal. Understanding the resistance mechanisms of bacteria against aminoglycosides is not only vital for improving the efficacy of this critically important group of antibiotics but also crucial for studying the molecular basis of translational fidelity. In this work, we analyzed Salmonella mutants evolved in the presence of the aminoglycoside streptomycin (Str) and identified a novel gene rimP to be involved in Str resistance. RimP is a ribosome assembly factor critical for the maturation of the 30S small subunit that binds Str. Deficiency in RimP increases resistance against Str and facilitates the development of even higher resistance. Deleting rimP decreases mistranslation and cellular uptake of Str and further impairs flagellar motility. Our work thus highlights a previously unknown mechanism of aminoglycoside resistance via defective ribosome assembly.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
| | - Yunyi Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, Maryland, USA
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5
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Hinnu M, Putrinš M, Kogermann K, Kaldalu N, Tenson T. Fluorescent reporters give new insights into antibiotics-induced nonsense and frameshift mistranslation. Sci Rep 2024; 14:6883. [PMID: 38519558 PMCID: PMC10959953 DOI: 10.1038/s41598-024-57597-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/20/2024] [Indexed: 03/25/2024] Open
Abstract
We developed a reporter system based on simultaneous expression of two fluorescent proteins: GFP as a reporter of the capacity of protein synthesis and mutated mScarlet-I as a reporter of translational errors. Because of the unique stop codons or frameshift mutations introduced into the mScarlet-I gene, red fluorescence was produced only after a mistranslation event. These reporters allowed us to estimate mistranslation at a single cell level using either flow cytometry or fluorescence microscopy. We found that laboratory strains of Escherichia coli are more prone to mistranslation compared to the clinical isolates. As relevant for uropathogenic E. coli, growth in human urine elevated translational frameshifting compared to standard laboratory media, whereas different standard media had a small effect on translational fidelity. Antibiotic-induced mistranslation was studied by using amikacin (aminoglycoside family) and azithromycin (macrolide family). Bactericidal amikacin induced preferably stop-codon readthrough at a moderate level. Bacteriostatic azithromycin on the other hand induced both frameshifting and stop-codon readthrough at much higher level. Single cell analysis revealed that fluorescent reporter-protein signal can be lost due to leakage from a fraction of bacteria in the presence of antibiotics, demonstrating the complexity of the antimicrobial activity.
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Affiliation(s)
- Mariliis Hinnu
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia.
| | - Marta Putrinš
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
- Institute of Pharmacy, University of Tartu, 50411, Tartu, Estonia
| | - Karin Kogermann
- Institute of Pharmacy, University of Tartu, 50411, Tartu, Estonia
| | - Niilo Kaldalu
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
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6
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McLellan JL, Hanson KK. Translation inhibition efficacy does not determine the Plasmodium berghei liver stage antiplasmodial efficacy of protein synthesis inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570699. [PMID: 38106175 PMCID: PMC10723475 DOI: 10.1101/2023.12.07.570699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Protein synthesis is a core cellular process, necessary throughout the complex lifecycle of Plasmodium parasites, thus specific translation inhibitors would be a valuable class of antimalarial drugs, capable of both treating symptomatic infections in the blood and providing chemoprotection by targeting the initial parasite population in the liver, preventing both human disease and parasite transmission back to the mosquito host. As increasing numbers of antiplasmodial compounds are identified that converge mechanistically at inhibition of cytoplasmic translation, regardless of molecular target or mechanism, it would be useful to gain deeper understanding of how their effectiveness as liver stage translation inhibitors relates to their chemoprotective potential. Here, we probed that relationship using the P. berghei-HepG2 liver stage infection model. Using o-propargyl puromycin-based labeling of the nascent proteome in P. berghei-infected HepG2 monolayers coupled with automated confocal feedback microscopy to generate unbiased, single parasite image sets of P. berghei liver stage translation, we determined translation inhibition EC50s for five compounds, encompassing parasite-specific aminoacyl tRNA synthetase inhibitors, compounds targeting the ribosome in both host and parasite, as well as DDD107498, which targets Plasmodium eEF2, and is a leading antimalarial candidate compound being clinically developed as cabamiquine. Compounds were then tested at equivalent effective concentrations to compare the parasite response to, and recovery from, a brief period of translation inhibition in early schizogony, with parasites followed up to 120 hours post-infection to assess liver stage antiplasmodial effects of the treatment. Our data conclusively show that translation inhibition efficacy per se does not determine a translation inhibitor's antiplasmodial efficacy. DDD107498 was the least effective translation inhibitor, yet exerted the strongest antimalarial effects at both 5x- and 10x EC50 concentrations. We show compound-specific heterogeneity in single parasite and population responses to translation inhibitor treatment, with no single metric strongly correlated to release of hepatic merozoites for all compound, demonstrate that DDD107498 is capable of exerting antiplasmodial effects on translationally arrested liver stage parasites, and uncover unexpected growth dynamics during the liver stage. Our results demonstrate that translation inhibition efficacy cannot function as a proxy for antiplasmodial effectiveness, and highlight the importance of exploring the ultimate, as well as proximate, mechanisms of action of these compounds on liver stage parasites.
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Affiliation(s)
- James L. McLellan
- University of Texas at San Antonio, Department of Molecular Microbiology and Immunology and STCEID, San Antonio TX, USA
| | - Kirsten K. Hanson
- University of Texas at San Antonio, Department of Molecular Microbiology and Immunology and STCEID, San Antonio TX, USA
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7
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Yaeger LN, French S, Brown ED, Côté JP, Burrows LL. Central metabolism is a key player in E. coli biofilm stimulation by sub-MIC antibiotics. PLoS Genet 2023; 19:e1011013. [PMID: 37917668 PMCID: PMC10645362 DOI: 10.1371/journal.pgen.1011013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/14/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
Exposure of Escherichia coli to sub-inhibitory antibiotics stimulates biofilm formation through poorly characterized mechanisms. Using a high-throughput Congo Red binding assay to report on biofilm matrix production, we screened ~4000 E. coli K12 deletion mutants for deficiencies in this biofilm stimulation response. We screened using three different antibiotics to identify core components of the biofilm stimulation response. Mutants lacking acnA, nuoE, or lpdA failed to respond to sub-MIC cefixime and novobiocin, implicating central metabolism and aerobic respiration in biofilm stimulation. These genes are members of the ArcA/B regulon-controlled by a respiration-sensitive two-component system. Mutants of arcA and arcB had a 'pre-activated' phenotype, where biofilm formation was already high relative to wild type in vehicle control conditions, and failed to increase further with the addition of sub-MIC cefixime. Using a tetrazolium dye and an in vivo NADH sensor, we showed spatial co-localization of increased metabolic activity with sub-lethal concentrations of the bactericidal antibiotics cefixime and novobiocin. Supporting a role for respiratory stress, the biofilm stimulation response to cefixime and novobiocin was inhibited when nitrate was provided as an alternative electron acceptor. Deletion of a gene encoding part of the machinery for respiring nitrate abolished its ameliorating effects, and nitrate respiration increased during growth with sub-MIC cefixime. Finally, in probing the generalizability of biofilm stimulation, we found that the stimulation response to translation inhibitors, unlike other antibiotic classes, was minimally affected by nitrate supplementation, suggesting that targeting the ribosome stimulates biofilm formation in distinct ways. By characterizing the biofilm stimulation response to sub-MIC antibiotics at a systems level, we identified multiple avenues for design of therapeutics that impair bacterial stress management.
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Affiliation(s)
- Luke N. Yaeger
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Eric D. Brown
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jean Philippe Côté
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Lori L. Burrows
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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8
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Yang KB, Cameranesi M, Gowder M, Martinez C, Shamovsky Y, Epshtein V, Hao Z, Nguyen T, Nirenstein E, Shamovsky I, Rasouly A, Nudler E. High-resolution landscape of an antibiotic binding site. Nature 2023; 622:180-187. [PMID: 37648864 PMCID: PMC10550828 DOI: 10.1038/s41586-023-06495-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 07/28/2023] [Indexed: 09/01/2023]
Abstract
Antibiotic binding sites are located in important domains of essential enzymes and have been extensively studied in the context of resistance mutations; however, their study is limited by positive selection. Using multiplex genome engineering1 to overcome this constraint, we generate and characterize a collection of 760 single-residue mutants encompassing the entire rifampicin binding site of Escherichia coli RNA polymerase (RNAP). By genetically mapping drug-enzyme interactions, we identify an alpha helix where mutations considerably enhance or disrupt rifampicin binding. We find mutations in this region that prolong antibiotic binding, converting rifampicin from a bacteriostatic to bactericidal drug by inducing lethal DNA breaks. The latter are replication dependent, indicating that rifampicin kills by causing detrimental transcription-replication conflicts at promoters. We also identify additional binding site mutations that greatly increase the speed of RNAP.Fast RNAP depletes the cell of nucleotides, alters cell sensitivity to different antibiotics and provides a cold growth advantage. Finally, by mapping natural rpoB sequence diversity, we discover that functional rifampicin binding site mutations that alter RNAP properties or confer drug resistance occur frequently in nature.
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Affiliation(s)
- Kevin B Yang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Maria Cameranesi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Manjunath Gowder
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Criseyda Martinez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yosef Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Vitaliy Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Thao Nguyen
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Eric Nirenstein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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9
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Aleksandrova EV, Wu KJY, Tresco BIC, Syroegin EA, Killeavy EE, Balasanyants SM, Svetlov MS, Gregory ST, Atkinson GC, Myers AG, Polikanov YS. Structural basis of Cfr-mediated antimicrobial resistance and mechanisms for its evasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559749. [PMID: 37808676 PMCID: PMC10557674 DOI: 10.1101/2023.09.27.559749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The ribosome is an essential drug target as many classes of clinically important antibiotics bind and inhibit its functional centers. The catalytic peptidyl transferase center (PTC) is targeted by the broadest array of inhibitors belonging to several chemical classes. One of the most abundant and clinically prevalent mechanisms of resistance to PTC-acting drugs is C8-methylation of the universally conserved adenine residue 2503 (A2503) of the 23S rRNA by the methyltransferase Cfr. Despite its clinical significance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. In this work, we developed a method to express a functionally-active Cfr-methyltransferase in the thermophilic bacterium Thermus thermophilus and report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-tRNAs. Our structures reveal that an allosteric rearrangement of nucleotide A2062 upon Cfr-methylation of A2503 is likely responsible for the inability of some PTC inhibitors to bind to the ribosome, providing additional insights into the Cfr resistance mechanism. Lastly, by determining the structures of the Cfr-methylated ribosome in complex with the antibiotics iboxamycin and tylosin, we provide the structural bases behind two distinct mechanisms of evading Cfr-mediated resistance.
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Affiliation(s)
- Elena V. Aleksandrova
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kelvin J. Y. Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ben I. C. Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Egor A. Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Erin E. Killeavy
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Samson M. Balasanyants
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Maxim S. Svetlov
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Steven T. Gregory
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA
| | - Gemma C. Atkinson
- Department of Experimental Medicine, University of Lund, Lund, Sweden
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Andrew G. Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yury S. Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
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10
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Gingras H, Peillard-Fiorente F, Godin C, Patron K, Leprohon P, Ouellette M. New Resistance Mutations Linked to Decreased Susceptibility to Solithromycin in Streptococcus pneumoniae Revealed by Chemogenomic Screens. Antimicrob Agents Chemother 2023; 67:e0039523. [PMID: 37409958 PMCID: PMC10433811 DOI: 10.1128/aac.00395-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/18/2023] [Indexed: 07/07/2023] Open
Abstract
Two strains of Streptococcus pneumoniae, one expressing the methyltransferase Erm(B) and the other negative for erm(B), were selected for solithromycin resistance in vitro either with direct drug selection or with chemical mutagenesis followed by drug selection. We obtained a series of mutants that we characterized by next-generation sequencing. We found mutations in various ribosomal proteins (L3, L4, L22, L32, and S4) and in the 23S rRNA. We also found mutations in subunits of the phosphate transporter, in the DEAD box helicase CshB, and in the erm(B)L leader peptide. All mutations were shown to decrease solithromycin susceptibility when transformed into sensitive isolates. Some of the genes derived from our in vitro screens were found to be mutated also in clinical isolates with decreased susceptibility to solithromycin. While many mutations were in coding sequences, some were found in regulatory regions. These included novel phenotypic mutations in the intergenic regions of the macrolide resistance locus mef(E)/mel and in the vicinity of the ribosome binding site of erm(B). Our screens highlighted that macrolide-resistant S. pneumoniae can easily acquire resistance to solithromycin, and they revealed many new phenotypic mutations.
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Affiliation(s)
- Hélène Gingras
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Flora Peillard-Fiorente
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Chantal Godin
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Kevin Patron
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
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11
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Wu KJY, Klepacki D, Mankin AS, Myers AG. A method for tritiation of iboxamycin permits measurement of its ribosomal binding. Bioorg Med Chem Lett 2023; 91:129364. [PMID: 37295615 PMCID: PMC10408240 DOI: 10.1016/j.bmcl.2023.129364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/25/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Hydrogen-tritium exchange is widely employed for radioisotopic labeling of molecules of biological interest but typically involves the metal-promoted exchange of sp2-hybridized carbon-hydrogen bonds, a strategy that is not directly applicable to the antibiotic iboxamycin, which possesses no such bonds. We show that ruthenium-induced 2'-epimerization of 2'-epi-iboxamycin in HTO (200 mCi) of low specific activity (10 Ci/g, 180 mCi/mmol) at 80 °C for 18 h affords after purification tritium-labeled iboxamycin (3.55 µCi) with a specific activity of 53 mCi/mmol. Iboxamycin displayed an apparent inhibition constant (Ki, app) of 41 ± 30 nM towards Escherichia coli ribosomes, binding approximately 70-fold more tightly than the antibiotic clindamycin (Ki, app = 2.7 ± 1.1 µM).
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Affiliation(s)
- Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dorota Klepacki
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Alexander S Mankin
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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12
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Chen CW, Leimer N, Syroegin EA, Dunand C, Bulman ZP, Lewis K, Polikanov YS, Svetlov MS. Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A. Nat Commun 2023; 14:4196. [PMID: 37452045 PMCID: PMC10349075 DOI: 10.1038/s41467-023-39653-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
The ever-growing rise of antibiotic resistance among bacterial pathogens is one of the top healthcare threats today. Although combination antibiotic therapies represent a potential approach to more efficiently combat infections caused by susceptible and drug-resistant bacteria, only a few known drug pairs exhibit synergy/cooperativity in killing bacteria. Here, we discover that well-known ribosomal antibiotics, hygromycin A (HygA) and macrolides, which target peptidyl transferase center and peptide exit tunnel, respectively, can act cooperatively against susceptible and drug-resistant bacteria. Remarkably, HygA slows down macrolide dissociation from the ribosome by 60-fold and enhances the otherwise weak antimicrobial activity of the newest-generation macrolide drugs known as ketolides against macrolide-resistant bacteria. By determining a set of high-resolution X-ray crystal structures of drug-sensitive wild-type and macrolide-resistant Erm-methylated 70S ribosomes in complex with three HygA-macrolide pairs, we provide a structural rationale for the binding cooperativity of these drugs and also uncover the molecular mechanism of overcoming Erm-type resistance by macrolides acting together with hygromycin A. Altogether our structural, biochemical, and microbiological findings lay the foundation for the subsequent development of synergistic antibiotic tandems with improved bactericidal properties against drug-resistant pathogens, including those expressing erm genes.
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Affiliation(s)
- Chih-Wei Chen
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Nadja Leimer
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Egor A Syroegin
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Clémence Dunand
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zackery P Bulman
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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13
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Jeremia L, Deprez BE, Dey D, Conn GL, Wuest WM. Ribosome-targeting antibiotics and resistance via ribosomal RNA methylation. RSC Med Chem 2023; 14:624-643. [PMID: 37122541 PMCID: PMC10131624 DOI: 10.1039/d2md00459c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
The rise of multidrug-resistant bacterial infections is a cause of global concern. There is an urgent need to both revitalize antibacterial agents that are ineffective due to resistance while concurrently developing new antibiotics with novel targets and mechanisms of action. Pathogen associated resistance-conferring ribosomal RNA (rRNA) methyltransferases are a growing threat that, as a group, collectively render a total of seven clinically-relevant ribosome-targeting antibiotic classes ineffective. Increasing frequency of identification and their growing prevalence relative to other resistance mechanisms suggests that these resistance determinants are rapidly spreading among human pathogens and could contribute significantly to the increased likelihood of a post-antibiotic era. Herein, with a view toward stimulating future studies to counter the effects of these rRNA methyltransferases, we summarize their prevalence, the fitness cost(s) to bacteria of their acquisition and expression, and current efforts toward targeting clinically relevant enzymes of this class.
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Affiliation(s)
- Learnmore Jeremia
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Benjamin E Deprez
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
| | - William M Wuest
- Department of Chemistry, Emory University 1515 Dickey Dr. Atlanta GA 30322 USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine 1510 Clifton Rd. Atlanta GA 30322 USA
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14
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Le D, Akiyama T, Weiss D, Kim M. Dissociation kinetics of small-molecule inhibitors in Escherichia coli is coupled to physiological state of cells. Commun Biol 2023; 6:223. [PMID: 36841892 PMCID: PMC9968327 DOI: 10.1038/s42003-023-04604-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/16/2023] [Indexed: 02/27/2023] Open
Abstract
Bioactive small-molecule inhibitors represent a treasure chest for future drugs. In vitro high-throughput screening is a common approach to identify the small-molecule inhibitors that bind tightly to purified targets. Here, we investigate the inhibitor-target binding/unbinding kinetics in E. coli cells using a benzimidazole-derivative DNA inhibitor as a model system. We find that its unbinding rate is not constant but depends on cell growth rate. This dependence is mediated by the cellular activity, forming a feedback loop with the inhibitor's activity. In accordance with this feedback, we find cell-to-cell heterogeneity in inhibitor-target interaction, leading to co-existence of two distinct subpopulations: actively growing cells that dissociate the inhibitors from the targets and non-growing cells that do not. We find similar heterogeneity for other clinical DNA inhibitors. Our studies reveal a mechanism that couples inhibitor-target kinetics to cell physiology and demonstrate the significant effect of this coupling on drug efficacy.
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Affiliation(s)
- Dai Le
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - Tatsuya Akiyama
- Department of Physics, Emory University, Atlanta, GA, 30322, USA
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
| | - David Weiss
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA, 30322, USA
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA
| | - Minsu Kim
- Department of Physics, Emory University, Atlanta, GA, 30322, USA.
- Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, GA, 30322, USA.
- Antibiotic Research Center, Emory University, Atlanta, GA, 30322, USA.
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15
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El-Khoury C, Mansour E, Yuliandra Y, Lai F, Hawkins BA, Du JJ, Sundberg EJ, Sluis-Cremer N, Hibbs DE, Groundwater PW. The role of adjuvants in overcoming antibacterial resistance due to enzymatic drug modification. RSC Med Chem 2022; 13:1276-1299. [PMID: 36439977 PMCID: PMC9667779 DOI: 10.1039/d2md00263a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/16/2022] [Indexed: 02/03/2023] Open
Abstract
Antibacterial resistance is a prominent issue with monotherapy often leading to treatment failure in serious infections. Many mechanisms can lead to antibacterial resistance including deactivation of antibacterial agents by bacterial enzymes. Enzymatic drug modification confers resistance to β-lactams, aminoglycosides, chloramphenicol, macrolides, isoniazid, rifamycins, fosfomycin and lincosamides. Novel enzyme inhibitor adjuvants have been developed in an attempt to overcome resistance to these agents, only a few of which have so far reached the market. This review discusses the different enzymatic processes that lead to deactivation of antibacterial agents and provides an update on the current and potential enzyme inhibitors that may restore bacterial susceptibility.
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Affiliation(s)
- Christy El-Khoury
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Elissar Mansour
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Yori Yuliandra
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Bryson A Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Jonathan J Du
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine Atlanta GA 30322 USA
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine Pittsburgh PA 15213 USA
| | - David E Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
| | - Paul W Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia
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16
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Swinney DC. Why medicines work. Pharmacol Ther 2022; 238:108175. [DOI: 10.1016/j.pharmthera.2022.108175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/27/2022]
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17
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Surette MD, Waglechner N, Koteva K, Wright GD. HelR is a helicase-like protein that protects RNA polymerase from rifamycin antibiotics. Mol Cell 2022; 82:3151-3165.e9. [PMID: 35907401 DOI: 10.1016/j.molcel.2022.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 03/15/2022] [Accepted: 06/12/2022] [Indexed: 10/16/2022]
Abstract
Rifamycin antibiotics such as rifampin are potent inhibitors of prokaryotic RNA polymerase (RNAP) used to treat tuberculosis and other bacterial infections. Although resistance arises in the clinic principally through mutations in RNAP, many bacteria possess highly specific enzyme-mediated resistance mechanisms that modify and inactivate rifamycins. The expression of these enzymes is controlled by a 19-bp cis-acting rifamycin-associated element (RAE). Guided by the presence of RAE sequences, we identify a helicase-like protein, HelR, in Streptomyces venezuelae that confers broad-spectrum rifamycin resistance. We show that HelR also promotes tolerance to rifamycins, enabling bacterial evasion of the toxic properties of these antibiotics. HelR forms a complex with RNAP and rescues transcription inhibition by displacing rifamycins from RNAP, thereby providing resistance by target protection . Furthermore, HelRs are broadly distributed in Actinobacteria, including several opportunistic Mycobacterial pathogens, offering yet another challenge for developing new rifamycin antibiotics.
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Affiliation(s)
- Matthew D Surette
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Nicholas Waglechner
- Toronto Invasive Bacterial Diseases Network, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Kalinka Koteva
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Gerard D Wright
- David Braley Center for Antibiotic Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
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18
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Synthesis and biological evaluation of antibacterial activity of novel clarithromycin derivatives incorporating 1,2,3-triazole moieties at the 4''- and 11-OH positions. Bioorg Chem 2022; 127:106020. [PMID: 35841669 DOI: 10.1016/j.bioorg.2022.106020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/20/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
Bacterial infection is still one of the diseases that threaten human health, and bacterial drug resistance is widespread worldwide. As a result, their eradication now largely relies on antibacterial drug discovery. Here, we reveal a novel approach to the development of 14-membered macrolide antibiotics by describing the design, synthesis, and evaluation of novel clarithromycin derivatives incorporating 1,2,3-triazole moieties at the 4''- and 11-OH positions. Using chemical synthesis, 35 clarithromycin derivatives were prepared, and their antibacterial properties were profiled. We found that compounds 8e-8h, 8l-8o, 8v, and 19d were as potent as azithromycin against Enterococcus faecalis ATCC29212. Furthermore, compounds 8c, 8d, 8n, and 8o showed slightly improved antibacterial activity (2-fold) against Acinetobacter baumannii ATCC19606 when compared with azithromycin and clarithromycin. In addition, compounds 8e, 8f, 8h, 8l, and 8v exhibited excellent antibacterial activity against Staphylococcus aureus ATCC43300, Staphylococcus aureus PR, and Streptococcus pneumoniae ER-2. These compounds were generally 64- to 128-fold more active than azithromycin, and 32- to 128-fold more active than clarithromycin. The results of molecular docking indicated that compound 8f may bind to the nucleotide residue A752 through hydrogen-bonding, hydrophobic, electrostatic, or π-π stacking interactions. The predicted ClogP data suggested that higher values of ClogP (>6.65) enhanced the antibacterial activity of compounds such as 8e, 8f, 8h, 8l, and 8v. The determination of the minimum bactericidal concentration showed that most of the tested compounds were bacteriostatic agents. From this study of bactericidal kinetics, we can conclude that compound 8f had a concentration- and time-dependent effect on the proliferation of Staphylococcus aureus ATCC43300. Finally, the results of the cytotoxicity assay showed that compound 8f exhibited no toxicity at the effective antibacterial concentration.
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19
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Alvarez-Manzo HS, Davidson RK, Van Cauwelaert de Wyels J, Cotten KL, Nguyen BH, Xiao M, Zhu Z, Anthony J, van Opijnen T, Davis KM. Yersinia pseudotuberculosis doxycycline tolerance strategies include modulating expression of genes involved in cell permeability and tRNA modifications. PLoS Pathog 2022; 18:e1010556. [PMID: 35576231 PMCID: PMC9135342 DOI: 10.1371/journal.ppat.1010556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/26/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022] Open
Abstract
Antibiotic tolerance is typically associated with a phenotypic change within a bacterial population, resulting in a transient decrease in antibiotic susceptibility that can contribute to treatment failure and recurrent infections. Although tolerant cells may emerge prior to treatment, the stress of prolonged antibiotic exposure can also promote tolerance. Here, we sought to determine how Yersinia pseudotuberculosis responds to doxycycline exposure, to then verify if these gene expression changes could promote doxycycline tolerance in culture and in our mouse model of infection. Only four genes were differentially regulated in response to a physiologically-relevant dose of doxycycline: osmB and ompF were upregulated, tusB and cnfy were downregulated; differential expression also occurred during doxycycline treatment in the mouse. ompF, tusB and cnfy were also differentially regulated in response to chloramphenicol, indicating these could be general responses to ribosomal inhibition. cnfy has previously been associated with persistence and was not a major focus here. We found deletion of the OmpF porin resulted in increased antibiotic accumulation, suggesting expression may promote diffusion of doxycycline out of the cell, while OsmB lipoprotein had a minor impact on antibiotic permeability. Overexpression of tusB significantly impaired bacterial survival in culture and in the mouse, suggesting that tRNA modification by tusB, and the resulting impacts on translational machinery, promotes survival during treatment with an antibiotic classically viewed as bacteriostatic. We believe this may be the first observation of bactericidal activity of doxycycline under physiological conditions, which was revealed by reversing tusB downregulation.
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Affiliation(s)
- Hector S. Alvarez-Manzo
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Robert K. Davidson
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jasper Van Cauwelaert de Wyels
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Katherine L. Cotten
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Benjamin H. Nguyen
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Melody Xiao
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Zeyu Zhu
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Jon Anthony
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Tim van Opijnen
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Kimberly Michele Davis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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20
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Brodiazhenko T, Turnbull KJ, Wu KJY, Takada H, Tresco BIC, Tenson T, Myers AG, Hauryliuk V. Synthetic oxepanoprolinamide iboxamycin is active against Listeria monocytogenes despite the intrinsic resistance mediated by VgaL/Lmo0919 ABCF ATPase. JAC Antimicrob Resist 2022; 4:dlac061. [PMID: 35733912 PMCID: PMC9204466 DOI: 10.1093/jacamr/dlac061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/17/2022] [Indexed: 01/15/2023] Open
Abstract
Background Listeriosis is a food-borne disease caused by the Gram-positive Bacillota (Firmicute) bacterium Listeria monocytogenes. Clinical L. monocytogenes isolates are often resistant to clinically used lincosamide clindamycin, thus excluding clindamycin as a viable treatment option. Objectives We have established newly developed lincosamide iboxamycin as a potential novel antilisterial agent. Methods We determined MICs of the lincosamides lincomycin, clindamycin and iboxamycin for L. monocytogenes, Enterococcus faecalis and Bacillus subtilis strains expressing synergetic antibiotic resistance determinants: ABCF ATPases that directly displace antibiotics from the ribosome and Cfr, a 23S rRNA methyltransferase that compromises antibiotic binding. For L. monocytogenes strains, either expressing VgaL/Lmo0919 or lacking the resistance factor, we performed time-kill kinetics and post-antibiotic effect assays. Results We show that the synthetic lincosamide iboxamycin is highly active against L. monocytogenes and can overcome the intrinsic lincosamide resistance mediated by VgaL/Lmo0919 ABCF ATPase. While iboxamycin is not bactericidal against L. monocytogenes, it displays a pronounced post-antibiotic effect, which is a valuable pharmacokinetic feature. We demonstrate that VmlR ABCF of B. subtilis grants significant (33-fold increase in MIC) protection from iboxamycin, while LsaA ABCF of E. faecalis grants an 8-fold protective effect. Furthermore, the VmlR-mediated iboxamycin resistance is cooperative with that mediated by the Cfr, resulting in up to a 512-fold increase in MIC. Conclusions While iboxamycin is a promising new antilisterial agent, our findings suggest that emergence and spread of ABCF ARE variants capable of defeating next-generation lincosamides in the clinic is possible and should be closely monitored.
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Affiliation(s)
| | | | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, MA , USA
| | - Hiraku Takada
- Department of Experimental Medicine, University of Lund , 221 84 Lund , Sweden
- Faculty of Life Sciences, Kyoto Sangyo University , Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555 , Japan
| | - Ben I C Tresco
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, MA , USA
| | - Tanel Tenson
- University of Tartu, Institute of Technology , 50411 Tartu , Estonia
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, MA , USA
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology , 50411 Tartu , Estonia
- Department of Experimental Medicine, University of Lund , 221 84 Lund , Sweden
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21
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Tirumalai MR, Rivas M, Tran Q, Fox GE. The Peptidyl Transferase Center: a Window to the Past. Microbiol Mol Biol Rev 2021; 85:e0010421. [PMID: 34756086 PMCID: PMC8579967 DOI: 10.1128/mmbr.00104-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In his 2001 article, "Translation: in retrospect and prospect," the late Carl Woese made a prescient observation that there was a need for the then-current view of translation to be "reformulated to become an all-embracing perspective about which 21st century Biology can develop" (RNA 7:1055-1067, 2001, https://doi.org/10.1017/s1355838201010615). The quest to decipher the origins of life and the road to the genetic code are both inextricably linked with the history of the ribosome. After over 60 years of research, significant progress in our understanding of how ribosomes work has been made. Particularly attractive is a model in which the ribosome may facilitate an ∼180° rotation of the CCA end of the tRNA from the A-site to the P-site while the acceptor stem of the tRNA would then undergo a translation from the A-site to the P-site. However, the central question of how the ribosome originated remains unresolved. Along the path from a primitive RNA world or an RNA-peptide world to a proto-ribosome world, the advent of the peptidyl transferase activity would have been a seminal event. This functionality is now housed within a local region of the large-subunit (LSU) rRNA, namely, the peptidyl transferase center (PTC). The PTC is responsible for peptide bond formation during protein synthesis and is usually considered to be the oldest part of the modern ribosome. What is frequently overlooked is that by examining the origins of the PTC itself, one is likely going back even further in time. In this regard, it has been proposed that the modern PTC originated from the association of two smaller RNAs that were once independent and now comprise a pseudosymmetric region in the modern PTC. Could such an association have survived? Recent studies have shown that the extant PTC is largely depleted of ribosomal protein interactions. It is other elements like metallic ion coordination and nonstandard base/base interactions that would have had to stabilize the association of RNAs. Here, we present a detailed review of the literature focused on the nature of the extant PTC and its proposed ancestor, the proto-ribosome.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Quyen Tran
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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22
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Synthesis of New Antibiotics Derivatives by the Photocatalytic Method: A Screening Research. Catalysts 2021. [DOI: 10.3390/catal11091102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The aim of our study was to assess the possibility of using the photocatalytic process conducted in the presence of TiO2 to obtain new stable derivatives of antibacterial drugs. The possibility of introducing hydroxyl, chlorine, or bromide groups into antibiotics molecules was investigated. The experiments were conducted in aqueous solutions in the presence of TiO2-P25 as a photocatalyst, Cl− and Br− ions, and antibiotics belonging to eight different chemical classes. All experiments were initiated by UVa radiation. The kinetics of photocatalytic reactions and their quantum yield were determined, and the stable products were identified. All of the antibiotics used in the experiments underwent a photocatalytic transformation, and the quantum yields were in the range from 0.63 to 22.3%. The presence of Br− or FeCl3 significantly increased the efficiency of the photocatalytic process performed in the presence of TiO2, although Br− ion also acted as an inhibitor. Potentially biologically active chlorine derivatives from Trimethoprim, Metronidazole, Chloramphenicol, and bromine derivatives from Trimethoprim, Amoxicillin were obtained under experimental conditions. The potentially inactive halogen derivatives of Sulfamethoxazole and hydroxyl derivatives described in the literature were also identified.
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23
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Structural basis for the tryptophan sensitivity of TnaC-mediated ribosome stalling. Nat Commun 2021; 12:5340. [PMID: 34504068 PMCID: PMC8429421 DOI: 10.1038/s41467-021-25663-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
Free L-tryptophan (L-Trp) stalls ribosomes engaged in the synthesis of TnaC, a leader peptide controlling the expression of the Escherichia coli tryptophanase operon. Despite extensive characterization, the molecular mechanism underlying the recognition and response to L-Trp by the TnaC-ribosome complex remains unknown. Here, we use a combined biochemical and structural approach to characterize a TnaC variant (R23F) with greatly enhanced sensitivity for L-Trp. We show that the TnaC-ribosome complex captures a single L-Trp molecule to undergo termination arrest and that nascent TnaC prevents the catalytic GGQ loop of release factor 2 from adopting an active conformation at the peptidyl transferase center. Importantly, the L-Trp binding site is not altered by the R23F mutation, suggesting that the relative rates of L-Trp binding and peptidyl-tRNA cleavage determine the tryptophan sensitivity of each variant. Thus, our study reveals a strategy whereby a nascent peptide assists the ribosome in detecting a small metabolite.
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24
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Beckert B, Leroy EC, Sothiselvam S, Bock LV, Svetlov MS, Graf M, Arenz S, Abdelshahid M, Seip B, Grubmüller H, Mankin AS, Innis CA, Vázquez-Laslop N, Wilson DN. Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics. Nat Commun 2021; 12:4466. [PMID: 34294725 PMCID: PMC8298421 DOI: 10.1038/s41467-021-24674-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/30/2021] [Indexed: 12/23/2022] Open
Abstract
Macrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.
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Affiliation(s)
- Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Elodie C Leroy
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France
| | | | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
| | - Maxim S Svetlov
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael Graf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Stefan Arenz
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Maha Abdelshahid
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Britta Seip
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - C Axel Innis
- Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ARNA, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Pessac, France.
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, USA.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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25
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Context-specific action of macrolide antibiotics on the eukaryotic ribosome. Nat Commun 2021; 12:2803. [PMID: 33990576 PMCID: PMC8121947 DOI: 10.1038/s41467-021-23068-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
Macrolide antibiotics bind in the nascent peptide exit tunnel of the bacterial ribosome and prevent polymerization of specific amino acid sequences, selectively inhibiting translation of a subset of proteins. Because preventing translation of individual proteins could be beneficial for the treatment of human diseases, we asked whether macrolides, if bound to the eukaryotic ribosome, would retain their context- and protein-specific action. By introducing a single mutation in rRNA, we rendered yeast Saccharomyces cerevisiae cells sensitive to macrolides. Cryo-EM structural analysis showed that the macrolide telithromycin binds in the tunnel of the engineered eukaryotic ribosome. Genome-wide analysis of cellular translation and biochemical studies demonstrated that the drug inhibits eukaryotic translation by preferentially stalling ribosomes at distinct sequence motifs. Context-specific action markedly depends on the macrolide structure. Eliminating macrolide-arrest motifs from a protein renders its translation macrolide-tolerant. Our data illuminate the prospects of adapting macrolides for protein-selective translation inhibition in eukaryotic cells.
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26
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Zieliński M, Park J, Sleno B, Berghuis AM. Structural and functional insights into esterase-mediated macrolide resistance. Nat Commun 2021; 12:1732. [PMID: 33741980 PMCID: PMC7979712 DOI: 10.1038/s41467-021-22016-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/19/2021] [Indexed: 01/08/2023] Open
Abstract
Macrolides are a class of antibiotics widely used in both medicine and agriculture. Unsurprisingly, as a consequence of their exensive usage a plethora of resistance mechanisms have been encountered in pathogenic bacteria. One of these resistance mechanisms entails the enzymatic cleavage of the macrolides' macrolactone ring by erythromycin esterases (Eres). The most frequently identified Ere enzyme is EreA, which confers resistance to the majority of clinically used macrolides. Despite the role Eres play in macrolide resistance, research into this family enzymes has been sparse. Here, we report the first three-dimensional structures of an erythromycin esterase, EreC. EreC is an extremely close homologue of EreA, displaying more than 90% sequence identity. Two structures of this enzyme, in conjunction with in silico flexible docking studies and previously reported mutagenesis data allowed for the proposal of a detailed catalytic mechanism for the Ere family of enzymes, labeling them as metal-independent hydrolases. Also presented are substrate spectrum assays for different members of the Ere family. The results from these assays together with an examination of residue conservation for the macrolide binding site in Eres, suggests two distinct active site archetypes within the Ere enzyme family.
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Affiliation(s)
- Michał Zieliński
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Jaeok Park
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Department of Biochemistry, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Barry Sleno
- Department of Biochemistry, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montréal, QC, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
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27
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Abstract
Bacterial cells utilize toxin-antitoxin systems to inhibit self-reproduction, while maintaining viability, when faced with environmental challenges. The activation of the toxin is often coupled to the induction of cellular response pathways, such as the stringent response, in response to multiple stress conditions. Under these conditions, the cell enters a quiescent state referred to as dormancy or persistence. How toxin activation triggers persistence and induces a systemic stress response in the alphaproteobacteria remains unclear. Here, we report that in Caulobacter, a hipA2-encoded bacterial toxin contributes to bacterial persistence by manipulating intracellular amino acid balance. HipA2 is a serine/threonine kinase that deactivates tryptophanyl-tRNA synthetase by phosphorylation, leading to stalled protein synthesis and the accumulation of free tryptophan. An increased level of tryptophan allosterically activates the adenylyltransferase activity of GlnE that, in turn, deactivates glutamine synthetase GlnA by adenylylation. The inactivation of GlnA promotes the deprivation of glutamine in the cell, which triggers a stringent response. By screening 69 stress conditions, we find that HipBA2 responds to multiple stress signals through the proteolysis of HipB2 antitoxin by the Lon protease and the release of active HipA2 kinase, revealing a molecular mechanism that allows disparate stress conditions to be sensed and funneled into a single response pathway.IMPORTANCE To overcome various environmental challenges, bacterial cells can enter a physiologically quiescent state, known as dormancy or persistence, which balances growth and viability. In this study, we report a new mechanism by which a toxin-antitoxin system responds to harsh environmental conditions or nutrient deprivation by orchestrating a dormant state while preserving viability. The hipA2-encoded kinase functions as a toxin in Caulobacter, inducing bacterial persistence by disturbing the intracellular tryptophan-glutamine balance. A nitrogen regulatory circuit can be regulated by the intracellular level of tryptophan, which mimics the allosteric role of glutamine in this feedback loop. The HipBA2 module senses different types of stress conditions by increasing the intracellular level of tryptophan, which in turn breaks the tryptophan-glutamine balance and induces glutamine deprivation. Our results reveal a molecular mechanism that allows disparate environmental challenges to converge on a common pathway that results in a dormant state.
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An Analysis of the Novel Fluorocycline TP-6076 Bound to Both the Ribosome and Multidrug Efflux Pump AdeJ from Acinetobacter baumannii. mBio 2021; 13:e0373221. [PMID: 35100868 PMCID: PMC8805024 DOI: 10.1128/mbio.03732-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Antibiotic resistance among bacterial pathogens continues to pose a serious global health threat. Multidrug-resistant (MDR) strains of the Gram-negative organism Acinetobacter baumannii utilize a number of resistance determinants to evade current antibiotics. One of the major resistance mechanisms employed by these pathogens is the use of multidrug efflux pumps. These pumps extrude xenobiotics directly out of bacterial cells, resulting in treatment failures when common antibiotics are administered. Here, the structure of the novel tetracycline antibiotic TP-6076, bound to both the Acinetobacter drug efflux pump AdeJ and the ribosome from Acinetobacter baumannii, using single-particle cryo-electron microscopy (cryo-EM), is elucidated. In this work, the structure of the AdeJ-TP-6076 complex is solved, and we show that AdeJ utilizes a network of hydrophobic interactions to recognize this fluorocycline. Concomitant with this, we elucidate three structures of TP-6076 bound to the A. baumannii ribosome and determine that its binding is stabilized largely by electrostatic interactions. We then compare the differences in binding modes between TP-6076 and the related tetracycline antibiotic eravacycline in both targets. These differences suggest that modifications to the tetracycline core may be able to alter AdeJ binding while maintaining interactions with the ribosome. Together, this work highlights how different mechanisms are used to stabilize the binding of tetracycline-based compounds to unique bacterial targets and provides guidance for the future clinical development of tetracycline antibiotics. IMPORTANCE Treatment of antibiotic-resistant organisms such as A. baumannii represents an ongoing issue for modern medicine. The multidrug efflux pump AdeJ serves as a major resistance determinant in A. baumannii through its action of extruding antibiotics from the cell. In this work, we use cryo-EM to show how AdeJ recognizes the experimental tetracycline antibiotic TP-6076 and prevents this drug from interacting with the A. baumannii ribosome. Since AdeJ and the ribosome use different binding modes to stabilize interactions with TP-6076, exploiting these differences may guide future drug development for combating antibiotic-resistant A. baumannii and potentially other strains of MDR bacteria.
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29
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Ginn J, Jiang X, Sun S, Michino M, Huggins DJ, Mbambo Z, Jansen R, Rhee KY, Arango N, Lima CD, Liverton N, Imaeda T, Okamoto R, Kuroita T, Aso K, Stamford A, Foley M, Meinke PT, Nathan C, Bryk R. Whole Cell Active Inhibitors of Mycobacterial Lipoamide Dehydrogenase Afford Selectivity over the Human Enzyme through Tight Binding Interactions. ACS Infect Dis 2021; 7:435-444. [PMID: 33527832 PMCID: PMC7888283 DOI: 10.1021/acsinfecdis.0c00788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Tuberculosis remains a leading cause of death from a single bacterial infection
worldwide. Efforts to develop new treatment options call for expansion into an
unexplored target space to expand the drug pipeline and bypass resistance to current
antibiotics. Lipoamide dehydrogenase is a metabolic and antioxidant enzyme critical for
mycobacterial growth and survival in mice. Sulfonamide analogs were previously
identified as potent and selective inhibitors of mycobacterial lipoamide dehydrogenase
in vitro but lacked activity against whole mycobacteria. Here we
present the development of analogs with improved permeability, potency, and selectivity,
which inhibit the growth of Mycobacterium tuberculosis in axenic
culture on carbohydrates and within mouse primary macrophages. They increase
intrabacterial pyruvate levels, supporting their on-target activity within mycobacteria.
Distinct modalities of binding between the mycobacterial and human enzymes contribute to
improved potency and hence selectivity through induced-fit tight binding interactions
within the mycobacterial but not human enzyme, as indicated by kinetic analysis and
crystallography.
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Affiliation(s)
- John Ginn
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | | | - Shan Sun
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - Mayako Michino
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - David J. Huggins
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | | | | | | | - Nancy Arango
- Structural Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
| | - Christopher D. Lima
- Structural Biology Program, Sloan Kettering Institute, New York, New York 10065, United States
- Howard Hughes Medical Institute, New York, New York 10065, United States
| | - Nigel Liverton
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - Toshihiro Imaeda
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - Rei Okamoto
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - Takanobu Kuroita
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - Kazuyoshi Aso
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - Andrew Stamford
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - Michael Foley
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
| | - Peter T. Meinke
- Tri-Institutional Therapeutics Discovery Institute, New York, New York 10065, United States
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30
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Zhang L, He J, Bai L, Ruan S, Yang T, Luo Y. Ribosome-targeting antibacterial agents: Advances, challenges, and opportunities. Med Res Rev 2021; 41:1855-1889. [PMID: 33501747 DOI: 10.1002/med.21780] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/08/2020] [Accepted: 12/19/2020] [Indexed: 02/05/2023]
Abstract
Ribosomes, which synthesize proteins, are critical organelles for the survival and growth of bacteria. About 60% of approved antibiotics discovered so far combat pathogenic bacteria by targeting ribosomes. However, several issues, such as drug resistance and toxicity, have impeded the clinical use of ribosome-targeting antibiotics. Moreover, the complexity of the bacteria ribosome structure has retarded the discovery of new ribosome-targeting agents that are considered as the key to the drug-resistance and toxicity. To deal with these challenges, efforts such as medicinal chemistry optimization, combination treatment, and new drug delivery system have been developed. But not enough, the development of structural biology and new screening methods bring powerful tools, such as cryo-electron microscopy technology, advanced computer-aided drug design, and cell-free in vitro transcription/translation systems, for the discovery of novel ribosome-targeting antibiotics. Thus, in this paper, we overview the research on different aspects of bacterial ribosomes, especially focus on discussing the challenges in the discovery of ribosome-targeting antibacterial drugs and advances made to address issues such as drug-resistance and selectivity, which, we believe, provide perspectives for the discovery of novel antibiotics.
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Affiliation(s)
- Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Jun He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Lang Bai
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shihua Ruan
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Laboratory of Human Diseases and Immunotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China.,Institute of Immunology and Inflammation, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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31
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Dong HJ, Zhang R, Kuang Y, Wang XJ. Selective regulation in ribosome biogenesis and protein production for efficient viral translation. Arch Microbiol 2020; 203:1021-1032. [PMID: 33124672 PMCID: PMC7594972 DOI: 10.1007/s00203-020-02094-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/18/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022]
Abstract
As intracellular parasites, viruses depend heavily on host cell structures and their functions to complete their life cycle and produce new viral particles. Viruses utilize or modulate cellular translational machinery to achieve efficient replication; the role of ribosome biogenesis and protein synthesis in viral replication particularly highlights the importance of the ribosome quantity and/or quality in controlling viral protein synthesis. Recently reported studies have demonstrated that ribosome biogenesis factors (RBFs) and ribosomal proteins (RPs) act as multifaceted regulators in selective translation of viral transcripts. Here we summarize the recent literature on RBFs and RPs and their association with subcellular redistribution, post-translational modification, enzyme catalysis, and direct interaction with viral proteins. The advances described in this literature establish a rationale for targeting ribosome production and function in the design of the next generation of antiviral agents.
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Affiliation(s)
- Hui-Jun Dong
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Rui Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Yu Kuang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Xiao-Jia Wang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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32
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Nugroho ADW, Kleerebezem M, Bachmann H. A Novel Method for Long-Term Analysis of Lactic Acid and Ammonium Production in Non-growing Lactococcus lactis Reveals Pre-culture and Strain Dependence. Front Bioeng Biotechnol 2020; 8:580090. [PMID: 33163481 PMCID: PMC7580867 DOI: 10.3389/fbioe.2020.580090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/15/2020] [Indexed: 01/25/2023] Open
Abstract
In various (industrial) conditions, cells are in a non-growing but metabolically active state in which de novo protein synthesis capacity is limited. The production of a metabolite by such non-growing cells is dependent on the cellular condition and enzyme activities, such as the amount, stability, and degradation of the enzyme(s). For industrial fermentations in which the metabolites of interest are mainly formed after cells enter the stationary phase, the investigation of prolonged metabolite production is of great importance. However, current batch model systems do not allow prolonged measurements due to metabolite accumulation driving product-inhibition. Here we developed a protocol that allows high-throughput metabolic measurements to be followed in real-time over extended periods (weeks). As a validation model, sugar utilization and arginine consumption by a low density of translationally blocked Lactococcus lactis was designed in a defined medium. In this system L. lactis MG1363 was compared with its derivative HB60, a strain described to achieve higher metabolic yield through a shift toward heterofermentative metabolism. The results showed that in a non-growing state HB60 is able to utilize more arginine than MG1363, and for both strains the decay of the measured activities were dependent on pre-culture conditions. During the first 5 days of monitoring a ∼25-fold decrease in acidification rate was found for strain HB60 as compared to a ∼20-fold decrease for strain MG1363. Such measurements are relevant for the understanding of microbial metabolism and for optimizing applications in which cells are frequently exposed to long-term suboptimal conditions, such as microbial cell factories, fermentation ripening, and storage survival.
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Affiliation(s)
- Avis Dwi Wahyu Nugroho
- TiFN, Wageningen, Netherlands.,Health Department, NIZO Food Research, Ede, Netherlands.,Laboratory of Host-Microbe Interactomics, Wageningen University and Research Centers, Wageningen, Netherlands
| | - Michiel Kleerebezem
- TiFN, Wageningen, Netherlands.,Laboratory of Host-Microbe Interactomics, Wageningen University and Research Centers, Wageningen, Netherlands
| | - Herwig Bachmann
- TiFN, Wageningen, Netherlands.,Health Department, NIZO Food Research, Ede, Netherlands.,Systems Biology Lab, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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33
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Tsakou F, Jersie-Christensen R, Jenssen H, Mojsoska B. The Role of Proteomics in Bacterial Response to Antibiotics. Pharmaceuticals (Basel) 2020; 13:E214. [PMID: 32867221 PMCID: PMC7559545 DOI: 10.3390/ph13090214] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
For many years, we have tried to use antibiotics to eliminate the persistence of pathogenic bacteria. However, these infectious agents can recover from antibiotic challenges through various mechanisms, including drug resistance and antibiotic tolerance, and continue to pose a global threat to human health. To design more efficient treatments against bacterial infections, detailed knowledge about the bacterial response to the commonly used antibiotics is required. Proteomics is a well-suited and powerful tool to study molecular response to antimicrobial compounds. Bacterial response profiling from system-level investigations could increase our understanding of bacterial adaptation, the mechanisms behind antibiotic resistance and tolerance development. In this review, we aim to provide an overview of bacterial response to the most common antibiotics with a focus on the identification of dynamic proteome responses, and through published studies, to elucidate the formation mechanism of resistant and tolerant bacterial phenotypes.
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Affiliation(s)
| | | | | | - Biljana Mojsoska
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark; (F.T.); (R.J.-C.); (H.J.)
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34
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Discrimination between G/C Binding Sites by Olivomycin A Is Determined by Kinetics of the Drug-DNA Interaction. Int J Mol Sci 2020; 21:ijms21155299. [PMID: 32722584 PMCID: PMC7432603 DOI: 10.3390/ijms21155299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022] Open
Abstract
Olivomycin A (OA) exerts its cytotoxic potency due to binding to the minor groove of the G/C-rich DNA and interfering with replication and transcription. Screening of the complete set of tetranucleotide G/C sites by electrophoretic mobility gel shift assay (EMSA) revealed that the sites containing central GC or GG dinucleotides were able to bind OA, whereas the sites with the central CG dinucleotide were not. However, studies of equilibrium OA binding in solution by fluorescence, circular dichroism and isothermal titration calorimetry failed to confirm the sequence preference of OA, indicating instead a similar type of complex and comparable affinity of OA to all G/C binding sites. This discrepancy was resolved by kinetics analysis of the drug–DNA interaction: the dissociation rate significantly differed between SGCS, SGGS and SCGS sites (S stands for G or C), thereby explaining the disintegration of the complexes during EMSA. The functional relevance of the revealed differential kinetics of OA–DNA interaction was demonstrated in an in vitro transcription assay. These findings emphasize the crucial role of kinetics in the mechanism of OA action and provide an important approach to the screening of new drug candidates.
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35
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Pichkur EB, Paleskava A, Tereshchenkov AG, Kasatsky P, Komarova ES, Shiriaev DI, Bogdanov AA, Dontsova OA, Osterman IA, Sergiev PV, Polikanov YS, Myasnikov AG, Konevega AL. Insights into the improved macrolide inhibitory activity from the high-resolution cryo-EM structure of dirithromycin bound to the E. coli 70S ribosome. RNA (NEW YORK, N.Y.) 2020; 26:715-723. [PMID: 32144191 PMCID: PMC7266154 DOI: 10.1261/rna.073817.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/27/2019] [Indexed: 05/05/2023]
Abstract
Macrolides are one of the most successful and widely used classes of antibacterials, which kill or stop the growth of pathogenic bacteria by binding near the active site of the ribosome and interfering with protein synthesis. Dirithromycin is a derivative of the prototype macrolide erythromycin with additional hydrophobic side chain. In our recent study, we have discovered that the side chain of dirithromycin forms lone pair-π stacking interaction with the aromatic imidazole ring of the His69 residue in ribosomal protein uL4 of the Thermus thermophilus 70S ribosome. In the current work, we found that neither the presence of the side chain, nor the additional contact with the ribosome, improve the binding affinity of dirithromycin to the ribosome. Nevertheless, we found that dirithromycin is a more potent inhibitor of in vitro protein synthesis in comparison with its parent compound, erythromycin. Using high-resolution cryo-electron microscopy, we determined the structure of the dirithromycin bound to the translating Escherichia coli 70S ribosome, which suggests that the better inhibitory properties of the drug could be rationalized by the side chain of dirithromycin pointing into the lumen of the nascent peptide exit tunnel, where it can interfere with the normal passage of the growing polypeptide chain.
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Affiliation(s)
- Evgeny B Pichkur
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- National Research Center "Kurchatov Institute," Moscow, 123182, Russia
| | - Alena Paleskava
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Andrey G Tereshchenkov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Pavel Kasatsky
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
| | - Ekaterina S Komarova
- Department of Bioengineering and Bioinformatics and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Dmitrii I Shiriaev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Alexey A Bogdanov
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Olga A Dontsova
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Ilya A Osterman
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Petr V Sergiev
- Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia
| | - Yury S Polikanov
- Departments of Biological Sciences and Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Alexander G Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
- Centre for Integrative Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, Illkirch, 67404, France
| | - Andrey L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute," Gatchina, 188300, Russia
- National Research Center "Kurchatov Institute," Moscow, 123182, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
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36
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Davoodi S, Daryaee F, Chang A, Walker SG, Tonge PJ. Correlating Drug-Target Residence Time and Post-antibiotic Effect: Insight into Target Vulnerability. ACS Infect Dis 2020; 6:629-636. [PMID: 32011855 DOI: 10.1021/acsinfecdis.9b00484] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Target vulnerability correlates the level of drug-target engagement required to generate a pharmacological response. High vulnerability targets are those that require only a relatively small fraction of occupancy to achieve the desired pharmacological outcome, whereas low vulnerability targets require high levels of engagement. Here, we demonstrate that the slope of the correlation between drug-target residence time and the post-antibiotic effect (PAE) can be used to define the vulnerability of bacterial targets. For macrolides, a steep slope is observed between residence time on the E. coli ribosome and the PAE, indicating that the ribosome is a highly vulnerable drug target. The analysis of the residence time-PAE data for erythromycin, azithromycin, spiramycin, and telithromycin using a mechanistic pharmacokinetic-pharmacodynamic model that integrates drug-target kinetics into predictions of drug activity lead to the successful prediction of the cellular PAE for tylosin, which has the longest residence time (7.1 h) and PAE (5.8 h). Although the macrolide data support a connection between residence time, PAE, and bactericidality, many bactericidal β-lactam antibiotics do not give a PAE, illustrating the role of factors such as protein resynthesis in the expression of target vulnerability.
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Abstract
This article describes 20 years of research that investigated a second novel target for ribosomal antibiotics, the biogenesis of the two subunits. Over that period, we have examined the effect of 52 different antibiotics on ribosomal subunit formation in six different microorganisms. Most of the antimicrobials we have studied are specific, preventing the formation of only the subunit to which they bind. A few interesting exceptions have also been observed. Forty-one research publications and a book chapter have resulted from this investigation. This review will describe the methodology we used and the fit of our results to a hypothetical model. The model predicts that inhibition of subunit assembly and translation are equivalent targets for most of the antibiotics we have investigated.
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Affiliation(s)
- W Scott Champney
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614, USA
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38
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A long-distance rRNA base pair impacts the ability of macrolide antibiotics to kill bacteria. Proc Natl Acad Sci U S A 2020; 117:1971-1975. [PMID: 31932436 PMCID: PMC6995004 DOI: 10.1073/pnas.1918948117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bactericidal activity of macrolide antibiotics correlates with the presence of an extended alkyl-aryl side chain, which accounts for their slow departure rate from the ribosome. Here, we found that the base pair between 23S ribosomal RNA (rRNA) nucleotides 752 and 2609 located in the macrolide binding site is important for the ribosome functionality and for establishing the unique interactions with the extended side chain of macrolide antibiotics. Disruption of the 752-2609 base pair accelerates the departure of extended macrolides from the ribosome and reduces their cidality. Our results demonstrate that not only the chemical features of the antibiotic, but also the structure of the target site contribute to the ability of the inhibitor to kill bacteria. While most of the ribosome-targeting antibiotics are bacteriostatic, some members of the macrolide class demonstrate considerable bactericidal activity. We previously showed that an extended alkyl-aryl side chain is the key structural element determining the macrolides’ slow dissociation from the ribosome and likely accounts for the antibiotics’ cidality. In the nontranslating Escherichia coli ribosome, the extended side chain of macrolides interacts with 23S ribosomal RNA (rRNA) nucleotides A752 and U2609, that were proposed to form a base pair. However, the existence of this base pair in the translating ribosome, its possible functional role, and its impact on the binding and cidality of the antibiotic remain unknown. By engineering E. coli cells carrying individual and compensatory mutations at the 752 and 2609 rRNA positions, we show that integrity of the base pair helps to modulate the ribosomal response to regulatory nascent peptides, determines the slow dissociation rate of the extended macrolides from the ribosome, and increases their bactericidal effect. Our findings demonstrate that the ability of antibiotics to kill bacterial cells relies not only on the chemical nature of the inhibitor, but also on structural features of the target.
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39
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Janas A, Przybylski P. 14- and 15-membered lactone macrolides and their analogues and hybrids: structure, molecular mechanism of action and biological activity. Eur J Med Chem 2019; 182:111662. [DOI: 10.1016/j.ejmech.2019.111662] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/12/2019] [Accepted: 08/29/2019] [Indexed: 11/15/2022]
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40
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Wolf NM, Lee H, Choules MP, Pauli GF, Phansalkar R, Anderson JR, Gao W, Ren J, Santarsiero BD, Lee H, Cheng J, Jin YY, Ho NA, Duc NM, Suh JW, Abad-Zapatero C, Cho S. High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads. ACS Infect Dis 2019; 5:829-840. [PMID: 30990022 DOI: 10.1021/acsinfecdis.8b00276] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Addressing the urgent need to develop novel drugs against drug-resistant Mycobacterium tuberculosis ( M. tb) strains, ecumicin (ECU) and rufomycin I (RUFI) are being explored as promising new leads targeting cellular proteostasis via the caseinolytic protein ClpC1. Details of the binding topology and chemical mode of (inter)action of these cyclopeptides help drive further development of novel potency-optimized entities as tuberculosis drugs. ClpC1 M. tb protein constructs with mutations driving resistance to ECU and RUFI show reduced binding affinity by surface plasmon resonance (SPR). Despite certain structural similarities, ECU and RUFI resistant mutation sites did not overlap in their SPR binding patterns. SPR competition experiments show ECU prevents RUFI binding, whereas RUFI partially inhibits ECU binding. The X-ray structure of the ClpC1-NTD-RUFI complex reveals distinct differences compared to the previously reported ClpC1-NTD-cyclomarin A structure. Surprisingly, the complex structure revealed that the epoxide moiety of RUFI opened and covalently bound to ClpC1-NTD via the sulfur atom of Met1. Furthermore, RUFI analogues indicate that the epoxy group of RUFI is critical for binding and bactericidal activity. The outcomes demonstrate the significance of ClpC1 as a novel target and the importance of SAR analysis of identified macrocyclic peptides for drug discovery.
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Affiliation(s)
- Nina M. Wolf
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Hyun Lee
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Biophysics Core at the Research Resource Center, University of Illinois at Chicago, 1100 S. Ashland Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Mary P. Choules
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Guido F. Pauli
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Rasika Phansalkar
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jeffrey R. Anderson
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Wei Gao
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
| | - Jinhong Ren
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Bernard D. Santarsiero
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Hanki Lee
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Jinhua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Ying-Yu Jin
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Ngoc Anh Ho
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Nguyen Minh Duc
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
- Division of Bioscience and Bioinformatics, College of Natural Sciences, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 17058, Republic of Korea
| | - Celerino Abad-Zapatero
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
- Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, 900 S. Ashland Street, Chicago, Illinois 60612, United States
| | - Sanghyun Cho
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, Illinois 60612, United States
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41
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ITC Studies of Ribosome/Antibiotics Interactions. Methods Mol Biol 2019. [PMID: 30929237 DOI: 10.1007/978-1-4939-9179-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The fight against multiresistant bacteria responsible for nosocomial diseases has recently been classified as an absolute priority by the World Health Organization. For some organisms, priority status has even been assessed as critical, as almost all currently available antibiotics are now inefficient against these "super-bacteria." Ribosome is a major target of several antibiotics, and extensive biochemical and structural studies led to a better understanding of the mechanism of action of drugs targeting translation (Blair et al., Nat Rev Microbiol 13:42-51, 2015; Lin et al., Annu Rev Biochem 87:451-478, 2018; Wilson, Nat Rev Microbiol 12:35-48, 2014; Yonath, Annu Rev Biochem 74:649-79, 2005). However, our knowledge regarding thermodynamic data of compounds targeting the ribosome, which are yet essential for a complete understanding of translation inhibition mechanisms by drugs, is still very poor.In this chapter we describe the use of ITC microcalorimetry to investigate the binding of bacterial ribosome to two antibiotics targeting the peptide tunnel: macrolides and proline-rich antimicrobial peptides (PrAMPs). This strategy yields reliable and artifact-free binding parameters for antibiotics and provides an original view on ribosome/antibiotics interactions.
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42
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Tan YJ, Tan YS, Yeo CI, Chew J, Tiekink ERT. In vitro anti-bacterial and time kill evaluation of binuclear tricyclohexylphosphanesilver(I) dithiocarbamates, {Cy 3PAg(S 2CNRR')} 2. J Inorg Biochem 2019; 192:107-118. [PMID: 30640150 DOI: 10.1016/j.jinorgbio.2018.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/27/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022]
Abstract
Four binuclear phosphanesilver(I) dithiocarbamates, {cyclohexyl3PAg(S2CNRR')}2 for R = R' = Et (1), CH2CH2 (2), CH2CH2OH (3) and R = Me, R' = CH2CH2OH (4) have been synthesised and characterised by spectroscopy and crystallography, and feature tri-connective, μ2-bridging dithiocarbamate ligands and distorted tetrahedral geometries based on PS3 donor sets. The compounds were evaluated for anti-bacterial activity against a total of 12 clinically important pathogens. Based on minimum inhibitory concentration (MIC) and cell viability tests (human embryonic kidney cells, HEK 293), 1-4 are specifically active against Gram-positive bacteria while demonstrating low toxicity; 3 and 4 are active against methicillin resistant S. aureus (MRSA). Across the series, 4 was most effective and was more active than the standard anti-biotic chloramphenicol. Time kill assays reveal 1-4 to exhibit both time- and concentration-dependent pharmacokinetics against susceptible bacteria. Compound 4 demonstrates rapid (within 2 h) bactericidal activity at 1 and 2 × MIC to reach a maximum decrease of 5.2 log10 CFU/mL against S. aureus (MRSA).
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Affiliation(s)
- Yi Jiun Tan
- Research Centre for Crystalline Materials, School of Science and Technology, Sunway University, No. 5 Jalan Universiti, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia; Department of Biological Sciences, School of Science and Technology, Sunway University, No. 5 Jalan Universiti, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Yee Seng Tan
- Research Centre for Crystalline Materials, School of Science and Technology, Sunway University, No. 5 Jalan Universiti, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Chien Ing Yeo
- Research Centre for Crystalline Materials, School of Science and Technology, Sunway University, No. 5 Jalan Universiti, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Jactty Chew
- Department of Biological Sciences, School of Science and Technology, Sunway University, No. 5 Jalan Universiti, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Edward R T Tiekink
- Research Centre for Crystalline Materials, School of Science and Technology, Sunway University, No. 5 Jalan Universiti, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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43
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Park JW, Yoon YJ. Recent advances in the discovery and combinatorial biosynthesis of microbial 14-membered macrolides and macrolactones. J Ind Microbiol Biotechnol 2018; 46:445-458. [PMID: 30415291 DOI: 10.1007/s10295-018-2095-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/19/2018] [Indexed: 01/05/2023]
Abstract
Macrolides, especially 14-membered macrolides, are a valuable group of antibiotics that originate from various microorganisms. In addition to their antibacterial activity, newly discovered 14-membered macrolides exhibit other therapeutic potentials, such as anti-proliferative and anti-protistal activities. Combinatorial biosynthetic approaches will allow us to create structurally diversified macrolide analogs, which are especially important during the emerging post-antibiotic era. This review focuses on recent advances in the discovery of new 14-membered macrolides (also including macrolactones) from microorganisms and the current status of combinatorial biosynthetic approaches, including polyketide synthase (PKS) and post-PKS tailoring pathways, and metabolic engineering for improved production together with heterologous production of 14-membered macrolides.
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Affiliation(s)
- Je Won Park
- School of Biosystem and Biomedical Science, Korea University, Seoul, 02841, Republic of Korea
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea.
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44
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Vázquez-Laslop N, Mankin AS. How Macrolide Antibiotics Work. Trends Biochem Sci 2018; 43:668-684. [PMID: 30054232 PMCID: PMC6108949 DOI: 10.1016/j.tibs.2018.06.011] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/17/2018] [Accepted: 06/29/2018] [Indexed: 01/24/2023]
Abstract
Macrolide antibiotics inhibit protein synthesis by targeting the bacterial ribosome. They bind at the nascent peptide exit tunnel and partially occlude it. Thus, macrolides have been viewed as 'tunnel plugs' that stop the synthesis of every protein. More recent evidence, however, demonstrates that macrolides selectively inhibit the translation of a subset of cellular proteins, and that their action crucially depends on the nascent protein sequence and on the antibiotic structure. Therefore, macrolides emerge as modulators of translation rather than as global inhibitors of protein synthesis. The context-specific action of macrolides is the basis for regulating the expression of resistance genes. Understanding the details of the mechanism of macrolide action may inform rational design of new drugs and unveil important principles of translation regulation.
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Affiliation(s)
- Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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45
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Golkar T, Zieliński M, Berghuis AM. Look and Outlook on Enzyme-Mediated Macrolide Resistance. Front Microbiol 2018; 9:1942. [PMID: 30177927 PMCID: PMC6109786 DOI: 10.3389/fmicb.2018.01942] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 07/31/2018] [Indexed: 01/14/2023] Open
Abstract
Since their discovery in the early 1950s, macrolide antibiotics have been used in both agriculture and medicine. Specifically, macrolides such as erythromycin and azithromycin have found use as substitutes for β-lactam antibiotics in patients with penicillin allergies. Given the extensive use of this class of antibiotics it is no surprise that resistance has spread among pathogenic bacteria. In these bacteria different mechanisms of resistance have been observed. Frequently observed are alterations in the target of macrolides, i.e., the ribosome, as well as upregulation of efflux pumps. However, drug modification is also increasingly observed. Two classes of enzymes have been implicated in macrolide detoxification: macrolide phosphotransferases and macrolide esterases. In this review, we present a comprehensive overview on what is known about macrolide resistance with an emphasis on the macrolide phosphotransferase and esterase enzymes. Furthermore, we explore how this information can assist in addressing resistance to macrolide antibiotics.
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Affiliation(s)
- Tolou Golkar
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Michał Zieliński
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montreal, QC, Canada.,Department of Microbiology & Immunology, McGill University, Montreal, QC, Canada
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46
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Fragments of the Nonlytic Proline-Rich Antimicrobial Peptide Bac5 Kill Escherichia coli Cells by Inhibiting Protein Synthesis. Antimicrob Agents Chemother 2018; 62:AAC.00534-18. [PMID: 29844040 DOI: 10.1128/aac.00534-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 05/19/2018] [Indexed: 11/20/2022] Open
Abstract
Unlike most antimicrobial peptides (AMPs), the main mode of action of the subclass of proline-rich antimicrobial peptides (PrAMPs) is not based on disruption of the bacterial membrane. Instead, PrAMPs exploit the inner membrane transporters SbmA and YjiL/MdtM to pass through the bacterial membrane and enter the cytosol of specific Gram-negative bacteria, where they exert an inhibitory effect on protein synthesis. Despite sharing a high proline and arginine content with other characterized PrAMPs, the PrAMP Bac5 has a low sequence identity with them. Here we investigated the mode of action of three N-terminal Bac5 fragments, Bac5(1-15), Bac5(1-25), and Bac5(1-31). We show that Bac5(1-25) and Bac5(1-31) retained excellent antimicrobial activity toward Escherichia coli and low toxicity toward eukaryotic cells, whereas Bac5(1-15) was inactive. Bac5(1-25) and Bac5(1-31) inhibited bacterial protein synthesis in vitro and in vivo Competition assays suggested that the binding site of Bac5 is within the ribosomal tunnel, where it prevents the transition from the initiation to the elongation phase of translation, as reported for other PrAMPs, such as the bovine PrAMP Bac7. Surprisingly, unlike Bac7, Bac5(1-25) exhibited species-specific inhibition, being an excellent inhibitor of protein synthesis on E. coli ribosomes but a poor inhibitor on Thermus thermophilus ribosomes. This indicates that while Bac5 most likely has an overlapping binding site with Bac7, the mode of interaction is distinct, suggesting that Bac5 fragments may be interesting alternative lead compounds for the development of new antimicrobial agents.
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