Submit to Antibiotics Review for Antibiotics Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Inhibitors of the Translational Apparatus

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (31 March 2016) | Viewed by 122789

Share This Special Issue

Special Issue Editor

Prof. Dr. Claudio O. Gualerzi

E-Mail Website
Guest Editor

Laboratory of Genetics, University of Camerino, Camerino, Italy
Interests: translation initiation in bacteria; cold and nutritional stress in bacteria; antimicrobials targeting bacterial translational apparatus

Special Issue Information

Dear Colleagues,

This issue of Antibiotics is dedicated to the topic of the translational apparatus as antimicrobial target. Protein synthesis is an essential function in all living organisms and despite evolutionary conservation, the actors that take part in this process in bacteria, lower and higher eukaryotes display enough differences so as to make the translational apparatus an ideal target for antibiotics. Indeed, approximately half of all antimicrobials known so far, belonging to various classes of antibiotics, interfere with translational functions.

This special issue will summarize the current knowledge on bacterial and/or yeast protein synthesis and its inhibition by antimicrobials. Thus, research as well as review articles focused on the characterization of various aspects (e.g., therapeutic properties, mechanism of action, resistance mechanisms etc.) of antibiotics targeting one or more functions of the translational apparatus are invited.

To ensure that the issue contains high quality contributions submitted manuscripts will be peer-reviewed under my supervision.

Prof. Dr. Claudio O. Gualerzi
Guest Editor

Knud H. Nierhaus

Hans-Jörg Rheinberger, Max Planck Institute for the History of Science, Berlin

It is with deep sadness and grief that we learned of our friend and colleague Knud Hermann Nierhaus passing away on the 7^th of April, 2016. He died prematurely, unexpectedly, and quite suddenly on the eve of his 75^th birthday. We are to mourn a personality who devoted his life to research, while sharing it with his family and his friends. This Special Issue of Antibiotics is dedicated to his memory.

Knud was born in Bochum, Germany, in 1941. After having studied medicine at the Universities of Tübingen and Vienna, he received his doctoral degree in 1967. He then spent two years as a medical assistant in various hospitals, before he joined the Department of Heinz Günter Wittmann at the newly founded Max Planck Institute for Molecular Genetics in Berlin-Dahlem. There he continued his extended career as a group leader, and after his retirement, as a guest scientist from 2010 onward, as well as a guest scientist at the Charité Berlin. In addition, since his studies at the Technical University Berlin in 1976, he regularly taught as a professor of molecular biology. As visible signs of his international reputation, he became an Elected Member of the European Molecular Biology Organization in 1984, and he was named Adjunct Professor of Molecular Biology at the Lomonosov University in Moscow in 1999, Distinguished International Scholar at the University of Pennsylvania in 2008, and Dr. honoris causa at the University of Patras, Greece, in 2009.

Knud has made numerous and important contributions to the field of ribosome and protein biosynthesis research. He is particularly well remembered for his seminal work on ribosome assembly, his functional and structural analyses of the ribosomal elongation cycle including the peptidyl transferase reaction, his work on translational regulation, and the inhibition mechanisms of numerous antibiotics. Among his widely acknowledged achievements in the 1970s was the total reconstitution of the large subunit from E. coli ribosomes, which greatly helped to understand processes of molecular self-assembly more generally. During the 1980s and the 1990s, he established the three tRNA binding site-model of the ribosomal elongation cycle as a ubiquitous feature of protein synthesis in all organismal kingdoms. At the same time, he investigated the three-dimensional structure of the large bacterial ribosomal subunit by means of neutron scattering; and from the late 1990s onward, he has been deeply involved in the cryo-electron microscopic inspection of functional states of the ribosome, as well as the modulation of protein biosynthesis by non-standard factors under conditions of stress and starvation. Since his first great paper on the ribosomal binding protein of chloramphenicol in 1973, he kept a keen interest in the elucidation of the inhibition mechanisms of antibiotics that intervene in the biosynthesis of proteins throughout his career.

I had the opportunity and pleasure of being associated with the group of Knud Nierhaus throughout the 1980s, and to experience the excitement with which he relentlessly accompanied and stimulated our efforts. Still today, I am immensely grateful for this time of apprenticeship in such a lively and international environment. Knud was a great teacher in experimentation. The community of ribosomologists all over the world will miss his constant-stimulating presence, keep him in good memory, and his work in high esteem.

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

aminoacylation
transformylation
riboswitches
ribozymes
ribosomes
translational factors
mRNA
tRNA
rRNA
regulation
inhibition
antimicrobials
antibiotic resistance

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (11 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

8185 KiB

Open AccessArticle

Conformational Response of 30S-bound IF3 to A-Site Binders Streptomycin and Kanamycin

by Roberto Chulluncuy, Carlos Espiche, Jose Alberto Nakamoto, Attilio Fabbretti and Pohl Milón

Antibiotics 2016, 5(4), 38; https://doi.org/10.3390/antibiotics5040038 - 13 Dec 2016

Cited by 18 | Viewed by 6291

Abstract

Aminoglycoside antibiotics are widely used to treat infectious diseases. Among them, streptomycin and kanamycin (and derivatives) are of importance to battle multidrug-resistant (MDR) Mycobacterium tuberculosis. Both drugs bind the small ribosomal subunit (30S) and inhibit protein synthesis. Genetic, structural, and biochemical studies indicate that local and long-range conformational rearrangements of the 30S subunit account for this inhibition. Here, we use intramolecular FRET between the C- and N-terminus domains of the flexible IF3 to monitor real-time perturbations of their binding sites on the 30S platform. Steady and pre-steady state binding experiments show that both aminoglycosides bring IF3 domains apart, promoting an elongated state of the factor. Binding of Initiation Factor IF1 triggers closure of IF3 bound to the 30S complex, while both aminoglycosides revert the IF1-dependent conformation. Our results uncover dynamic perturbations across the 30S subunit, from the A-site to the platform, and suggest that both aminoglycosides could interfere with prokaryotic translation initiation by modulating the interaction between IF3 domains with the 30S platform. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Figure 1

3905 KiB

Open AccessArticle

The Novel Aminomethylcycline Omadacycline Has High Specificity for the Primary Tetracycline-Binding Site on the Bacterial Ribosome

by Corina G. Heidrich, Sanya Mitova, Andreas Schedlbauer, Sean R. Connell, Paola Fucini, Judith N. Steenbergen and Christian Berens

Antibiotics 2016, 5(4), 32; https://doi.org/10.3390/antibiotics5040032 - 22 Sep 2016

Cited by 30 | Viewed by 11097

Abstract

Omadacycline is an aminomethylcycline antibiotic with potent activity against many Gram-positive and Gram-negative pathogens, including strains carrying the major efflux and ribosome protection resistance determinants. This makes it a promising candidate for therapy of severe infectious diseases. Omadacycline inhibits bacterial protein biosynthesis and competes with tetracycline for binding to the ribosome. Its interactions with the 70S ribosome were, therefore, analyzed in great detail and compared with tigecycline and tetracycline. All three antibiotics are inhibited by mutations in the 16S rRNA that mediate resistance to tetracycline in Brachyspira hyodysenteriae, Helicobacter pylori, Mycoplasma hominis, and Propionibacterium acnes. Chemical probing with dimethyl sulfate and Fenton cleavage with iron(II)-complexes of the tetracycline derivatives revealed that each antibiotic interacts in an idiosyncratic manner with the ribosome. X-ray crystallography had previously revealed one primary binding site for tetracycline on the ribosome and up to five secondary sites. All tetracyclines analyzed here interact with the primary site and tetracycline also with two secondary sites. In addition, each derivative displays a unique set of non-specific interactions with the 16S rRNA. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Figure 1

2521 KiB

Open AccessArticle

Insights into the Stress Response Triggered by Kasugamycin in Escherichia coli

by Christian Müller, Lena Sokol, Oliver Vesper, Martina Sauert and Isabella Moll

Antibiotics 2016, 5(2), 19; https://doi.org/10.3390/antibiotics5020019 - 1 Jun 2016

Cited by 11 | Viewed by 6294

Abstract

The bacteriostatic aminoglycoside antibiotic kasugamycin inhibits protein synthesis at an initial step without affecting translation elongation. It binds to the mRNA track of the ribosome and prevents formation of the translation initiation complex on canonical mRNAs. In contrast, translation of leaderless mRNAs continues in the presence of the drug in vivo. Previously, we have shown that kasugamycin treatment in E. coli stimulates the formation of protein-depleted ribosomes that are selective for leaderless mRNAs. Here, we provide evidence that prolonged kasugamycin treatment leads to selective synthesis of specific proteins. Our studies indicate that leaderless and short-leadered mRNAs are generated by different molecular mechanisms including alternative transcription and RNA processing. Moreover, we provide evidence for ribosome heterogeneity in response to kasugamycin treatment by alteration of the modification status of the stalk proteins bL7/L12. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Figure 1

4024 KiB

Open AccessArticle

Ribosome Assembly as Antimicrobial Target

by Rainer Nikolay, Sabine Schmidt, Renate Schlömer, Elke Deuerling and Knud H. Nierhaus

Antibiotics 2016, 5(2), 18; https://doi.org/10.3390/antibiotics5020018 - 27 May 2016

Cited by 16 | Viewed by 10738

Abstract

Many antibiotics target the ribosome and interfere with its translation cycle. Since translation is the source of all cellular proteins including ribosomal proteins, protein synthesis and ribosome assembly are interdependent. As a consequence, the activity of translation inhibitors might indirectly cause defective ribosome assembly. Due to the difficulty in distinguishing between direct and indirect effects, and because assembly is probably a target in its own right, concepts are needed to identify small molecules that directly inhibit ribosome assembly. Here, we summarize the basic facts of ribosome targeting antibiotics. Furthermore, we present an in vivo screening strategy that focuses on ribosome assembly by a direct fluorescence based read-out that aims to identify and characterize small molecules acting as primary assembly inhibitors. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Figure 1

1611 KiB

Open AccessArticle

The Oligopeptide Permease Opp Mediates Illicit Transport of the Bacterial P-site Decoding Inhibitor GE81112

by Alessandro Maio, Letizia Brandi, Stefano Donadio and Claudio O. Gualerzi

Antibiotics 2016, 5(2), 17; https://doi.org/10.3390/antibiotics5020017 - 24 May 2016

Cited by 22 | Viewed by 6971

Abstract

GE81112 is a tetrapeptide antibiotic that binds to the 30S ribosomal subunit and specifically inhibits P-site decoding of the mRNA initiation codon by the fMet-tRNA anticodon. GE81112 displays excellent microbiological activity against some Gram-positive and Gram-negative bacteria in both minimal and complete, chemically defined, broth, but is essentially inactive in complete complex media. This is due to the presence of peptides that compete with the antibiotic for the oligopeptide permease system (Opp) responsible for its illicit transport into the bacterial cells as demonstrated in the cases of Escherichia coli and Bacillus subtilis. Mutations that inactivate the Opp system and confer GE81112 resistance arise spontaneously with a frequency of ca. 1 × 10⁻⁶, similar to that of the mutants resistant to tri-l-ornithine, a known Opp substrate. On the contrary, cells expressing extrachromosomal copies of the opp genes are extremely sensitive to GE81112 in rich medium and GE81112-resistant mutations affecting the molecular target of the antibiotic were not detected upon examining >10⁹ cells of this type. However, some mutations introduced in the 16S rRNA to confer kasugamycin resistance were found to reduce the sensitivity of the cells to GE81112. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Figure 1

1597 KiB

Open AccessArticle

Small Molecule Docking Supports Broad and Narrow Spectrum Potential for the Inhibition of the Novel Antibiotic Target Bacterial Pth1

by Paul P. Ferguson, W. Blake Holloway, William N. Setzer, Hana McFeeters and Robert L. McFeeters

Antibiotics 2016, 5(2), 16; https://doi.org/10.3390/antibiotics5020016 - 10 May 2016

Cited by 5 | Viewed by 6710

Abstract

Peptidyl-tRNA hydrolases (Pths) play ancillary yet essential roles in protein biosynthesis by recycling peptidyl-tRNA. In E. coli, inhibition of bacterial Pth1 leads to accumulation of peptidyl-tRNA, depletion of aminoacyl-tRNA, and cell death. Eukaryotes have multiple Pths and Pth1 knock out was shown to have no effect on viability in yeast. Thereby, bacterial Pth1 is a promising target for novel antibiotic development. With the abundance of Pth1 structural data, molecular docking was used for virtual screening of existing, commercially available antibiotics to map potential interactions with Pth enzymes. Overall, 83 compounds were docked to eight different bacterial Pth1 and three different Pth2 structures. A variety of compounds demonstrated favorable docking with Pths. Whereas, some compounds interacted favorably with all Pths (potential broad spectrum inhibition), more selective interactions were observed for Pth1 or Pth2 and even specificity for individual Pth1s. While the correlation between computational docking and experimentation still remains unknown, these findings support broad spectrum inhibition, but also point to the possibility of narrow spectrum Pth1 inhibition. Also suggested is that Pth1 can be distinguished from Pth2 by small molecule inhibitors. The findings support continued development of Pth1 as an antibiotic target. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Graphical abstract

Review

Jump to: Research

950 KiB

Open AccessReview

From Erythromycin to Azithromycin and New Potential Ribosome-Binding Antimicrobials

by Dubravko Jelić and Roberto Antolović

Antibiotics 2016, 5(3), 29; https://doi.org/10.3390/antibiotics5030029 - 1 Sep 2016

Cited by 144 | Viewed by 30646

Abstract

Macrolides, as a class of natural or semisynthetic products, express their antibacterial activity primarily by reversible binding to the bacterial 50S ribosomal subunits and by blocking nascent proteins’ progression through their exit tunnel in bacterial protein biosynthesis. Generally considered to be bacteriostatic, they may also be bactericidal at higher doses. The discovery of azithromycin from the class of macrolides, as one of the most important new drugs of the 20th century, is presented as an example of a rational medicinal chemistry approach to drug design, applying classical structure-activity relationship that will illustrate an impressive drug discovery success story. However, the microorganisms have developed several mechanisms to acquire resistance to antibiotics, including macrolide antibiotics. The primary mechanism for acquiring bacterial resistance to macrolides is a mutation of one or more nucleotides from the binding site. Although azithromycin is reported to show different, two-step process of the inhibition of ribosome function of some species, more detailed elaboration of that specific mode of action is needed. New macrocyclic derivatives, which could be more potent and less prone to escape bacterial resistance mechanisms, are also continuously evaluated. A novel class of antibiotic compounds—macrolones, which are derived from macrolides and comprise macrocyclic moiety, linker, and either free or esterified quinolone 3-carboxylic group, show excellent antibacterial potency towards key erythromycin-resistant Gram-positive and Gram-negative bacterial strains, with possibly decreased potential of bacterial resistance to macrolides. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Figure 1

4591 KiB

Open AccessReview

Ribosomal Antibiotics: Contemporary Challenges

by Tamar Auerbach-Nevo, David Baram, Anat Bashan, Matthew Belousoff, Elinor Breiner, Chen Davidovich, Giuseppe Cimicata, Zohar Eyal, Yehuda Halfon, Miri Krupkin, Donna Matzov, Markus Metz, Mruwat Rufayda, Moshe Peretz, Ophir Pick, Erez Pyetan, Haim Rozenberg, Moran Shalev-Benami, Itai Wekselman, Raz Zarivach, Ella Zimmerman, Nofar Assis, Joel Bloch, Hadar Israeli, Rinat Kalaora, Lisha Lim, Ofir Sade-Falk, Tal Shapira, Leena Taha-Salaime, Hua Tang and Ada Yonath Show full author list Hide full author list

Antibiotics 2016, 5(3), 24; https://doi.org/10.3390/antibiotics5030024 - 29 Jun 2016

Cited by 9 | Viewed by 8315

Abstract

Most ribosomal antibiotics obstruct distinct ribosomal functions. In selected cases, in addition to paralyzing vital ribosomal tasks, some ribosomal antibiotics are involved in cellular regulation. Owing to the global rapid increase in the appearance of multi-drug resistance in pathogenic bacterial strains, and to the extremely slow progress in developing new antibiotics worldwide, it seems that, in addition to the traditional attempts at improving current antibiotics and the intensive screening for additional natural compounds, this field should undergo substantial conceptual revision. Here, we highlight several contemporary issues, including challenging the common preference of broad-range antibiotics; the marginal attention to alterations in the microbiome population resulting from antibiotics usage, and the insufficient awareness of ecological and environmental aspects of antibiotics usage. We also highlight recent advances in the identification of species-specific structural motifs that may be exploited for the design and the creation of novel, environmental friendly, degradable, antibiotic types, with a better distinction between pathogens and useful bacterial species in the microbiome. Thus, these studies are leading towards the design of “pathogen-specific antibiotics,” in contrast to the current preference of broad range antibiotics, partially because it requires significant efforts in speeding up the discovery of the unique species motifs as well as the clinical pathogen identification. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Graphical abstract

418 KiB

Open AccessReview

Techniques for Screening Translation Inhibitors

by Ilya A. Osterman, Alexey A. Bogdanov, Olga A. Dontsova and Petr V. Sergiev

Antibiotics 2016, 5(3), 22; https://doi.org/10.3390/antibiotics5030022 - 24 Jun 2016

Cited by 7 | Viewed by 7378

Abstract

The machinery of translation is one of the most common targets of antibiotics. The development and screening of new antibiotics usually proceeds by testing antimicrobial activity followed by laborious studies of the mechanism of action. High-throughput methods for new antibiotic screening based on antimicrobial activity have become routine; however, identification of molecular targets is usually a challenge. Therefore, it is highly beneficial to combine primary screening with the identification of the mechanism of action. In this review, we describe a collection of methods for screening translation inhibitors, with a special emphasis on methods which can be performed in a high-throughput manner. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Figure 1

4326 KiB

Open AccessReview

Chloramphenicol Derivatives as Antibacterial and Anticancer Agents: Historic Problems and Current Solutions

by George P. Dinos, Constantinos M. Athanassopoulos, Dionissia A. Missiri, Panagiota C. Giannopoulou, Ioannis A. Vlachogiannis, Georgios E. Papadopoulos, Dionissios Papaioannou and Dimitrios L. Kalpaxis

Antibiotics 2016, 5(2), 20; https://doi.org/10.3390/antibiotics5020020 - 3 Jun 2016

Cited by 112 | Viewed by 20753

Abstract

Chloramphenicol (CAM) is the D-threo isomer of a small molecule, consisting of a p-nitrobenzene ring connected to a dichloroacetyl tail through a 2-amino-1,3-propanediol moiety. CAM displays a broad-spectrum bacteriostatic activity by specifically inhibiting the bacterial protein synthesis. In certain but important cases, it also exhibits bactericidal activity, namely against the three most common causes of meningitis, Haemophilus influenzae, Streptococcus pneumoniae and Neisseria meningitidis. Resistance to CAM has been frequently reported and ascribed to a variety of mechanisms. However, the most important concerns that limit its clinical utility relate to side effects such as neurotoxicity and hematologic disorders. In this review, we present previous and current efforts to synthesize CAM derivatives with improved pharmacological properties. In addition, we highlight potentially broader roles of these derivatives in investigating the plasticity of the ribosomal catalytic center, the main target of CAM. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Graphical abstract

524 KiB

Open AccessReview

Antibiotics and RNase P

by Denis Drainas

Antibiotics 2016, 5(2), 15; https://doi.org/10.3390/antibiotics5020015 - 6 May 2016

Cited by 6 | Viewed by 5745

Abstract

RNase P is an essential endonuclease in tRNA biogenesis, which generates the mature 5′-termini of tRNAs. Most forms of RNase P are ribonucleoproteins, i.e., they consist of an essential RNA and protein subunits. The catalytic function of ribonucleoprotein RNase P enzymes resides entirely in the RNA subunit. Its high structural and functional diversity among representatives of a vast variety of phylogenetic domains indicates that RNase P could serve as a molecular target and a useful screening system for the development of new drugs in the battle against bacterial drug resistance. Full article

(This article belongs to the Special Issue Inhibitors of the Translational Apparatus)

► Show Figures

Journal Menu

Journal Browser

Inhibitors of the Translational Apparatus

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (11 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI