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Antibiotics
Special Issues
Ribosomal Antibiotics: Recent Advances
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Ribosomal Antibiotics: Recent Advances

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

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 4394

Special Issue Editor

Dr. Miri Krupkin

E-Mail Website
Guest Editor
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
Interests: RNA; ribosome; antibiotics; antivirals; HIV; structural biology

Special Issue Information

Dear Colleagues,

The discovery and use of antibiotics have improved both longevity and quality of life. Ribosomal antibiotics comprise a major class of clinically available antibiotics, targeting more than a dozen different sites on both ribosomal subunits. Yet, the rise of antibiotic resistance poses a threat to their use for common infections, routine surgeries, and even modern agriculture. Understanding processes that contribute to the emerging resistance to antibiotics is an urgent need. Furthermore, this data is critical for the development of new antibiotics and for the design of antibiotics manufacturing, use, and disposal in the future. 

This Issue welcomes manuscript submissions, including original research articles, review articles, case series, and opinion papers. Specifically, work from the following fields of research is especially encouraged:

  • Resistance mechanisms of ribosomal antibiotics, including RNA modifications;
  • Organic and enzymatic synthesis and modification of ribosomal antibiotics;
  • In vitro and in situ structures of ribosomal antibiotics;
  • Discovery of new ribosomal antibiotics using both classical natural products and bioinformatics approaches;
  • Ribosomal antibiotics in producing bacteria;
  • Pathogen specificity of ribosomal antibiotics;
  • Ribosomal antibiotics in women’s and children’s health;
  • Clinical studies of ribosomal antibiotics and nosocomial pathogens;
  • Ribosomal antibiotics and their environmental impact;
  • Ribosomal antibiotics use in animals;
  • Ribosomal antibiotics in teaching and education.

Dr. Miri Krupkin
Guest Editor

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

  • ribosome
  • ribosomal antibiotics
  • antibiotic resistance
  • RNA modification
  • multi-drug resistant pathogens
  • antibiotic specificity

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Published Papers (1 paper)

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Research

23 pages, 11458 KiB  
Article
Comparative Assessment of Docking Programs for Docking and Virtual Screening of Ribosomal Oxazolidinone Antibacterial Agents
by McKenna E. Buckley, Audrey R. N. Ndukwe, Pramod C. Nair, Santu Rana, Kathryn E. Fairfull-Smith and Neha S. Gandhi
Antibiotics 2023, 12(3), 463; https://doi.org/10.3390/antibiotics12030463 - 24 Feb 2023
Cited by 5 | Viewed by 3939
Abstract
Oxazolidinones are a broad-spectrum class of synthetic antibiotics that bind to the 50S ribosomal subunit of Gram-positive and Gram-negative bacteria. Many crystal structures of the ribosomes with oxazolidinone ligands have been reported in the literature, facilitating structure-based design using methods such as molecular [...] Read more.
Oxazolidinones are a broad-spectrum class of synthetic antibiotics that bind to the 50S ribosomal subunit of Gram-positive and Gram-negative bacteria. Many crystal structures of the ribosomes with oxazolidinone ligands have been reported in the literature, facilitating structure-based design using methods such as molecular docking. It would be of great interest to know in advance how well docking methods can reproduce the correct ligand binding modes and rank these correctly. We examined the performance of five molecular docking programs (AutoDock 4, AutoDock Vina, DOCK 6, rDock, and RLDock) for their ability to model ribosomal–ligand interactions with oxazolidinones. Eleven ribosomal crystal structures with oxazolidinones as the ligands were docked. The accuracy was evaluated by calculating the docked complexes’ root-mean-square deviation (RMSD) and the program’s internal scoring function. The rankings for each program based on the median RMSD between the native and predicted were DOCK 6 > AD4 > Vina > RDOCK >> RLDOCK. Results demonstrate that the top-performing program, DOCK 6, could accurately replicate the ligand binding in only four of the eleven ribosomes due to the poor electron density of said ribosomal structures. In this study, we have further benchmarked the performance of the DOCK 6 docking algorithm and scoring in improving virtual screening (VS) enrichment using the dataset of 285 oxazolidinone derivatives against oxazolidinone binding sites in the S. aureus ribosome. However, there was no clear trend between the structure and activity of the oxazolidinones in VS. Overall, the docking performance indicates that the RNA pocket’s high flexibility does not allow for accurate docking prediction, highlighting the need to validate VS. protocols for ligand-RNA before future use. Later, we developed a re-scoring method incorporating absolute docking scores and molecular descriptors, and the results indicate that the descriptors greatly improve the correlation of docking scores and pMIC values. Morgan fingerprint analysis was also used, suggesting that DOCK 6 underpredicted molecules with tail modifications with acetamide, n-methylacetamide, or n-ethylacetamide and over-predicted molecule derivatives with methylamino bits. Alternatively, a ligand-based approach similar to a field template was taken, indicating that each derivative’s tail groups have strong positive and negative electrostatic potential contributing to microbial activity. These results indicate that one should perform VS. campaigns of ribosomal antibiotics with care and that more comprehensive strategies, including molecular dynamics simulations and relative free energy calculations, might be necessary in conjunction with VS. and docking. Full article
(This article belongs to the Special Issue Ribosomal Antibiotics: Recent Advances)
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