# Molecular mechanisms of action of ribosome-targeting antibiotics.

> **NIH NIH R01** · UNIVERSITY OF ILLINOIS AT CHICAGO · 2020 · $314,531

## Abstract

SUMMARY
Ribosome-targeting antibiotics are indispensable both as therapeutic agents and as tools for basic research. In
spite of the importance of these inhibitors, there are significant gaps in our understanding of the most
fundamental principles of their action. Most of them interfere with protein synthesis by blocking the functional
centers of the ribosome. Out of several functional centers, the catalytic peptidyl transferase center (PTC) and
the nascent peptide exit tunnel (NPET) are the sites targeted by the broadest array of inhibitors. In the proposed
project, we will explore the molecular mechanisms of action of the most basic PTC-targeting antibiotics and
macrolides – chloramphenicol (CHL) and erythromycin (ERY). Recent studies yielded the unexpected conclusion
that, in contrast to the general view of CHL and ERY as global and indiscriminate inhibitors, these antibiotics
interfere with translation in a context-specific manner indicating that our understanding of their mechanism of
action is incomplete and possibly even wrong. One way to obtain a clear explanation for the paradigm-shifting
phenomenon of context-specific activity of PTC-acting inhibitors and macrolides is to directly visualize them
within the ribosome complexes conducive to their action. Previous crystal structures uncovered how CHL and
ERY bind to the PTC and NPET of the vacant bacterial ribosome and therefore provide information that is
irrelevant for their context-specific activity. By determining the structures of CHL and ERY (as well as other PTC-
acting drugs and macrolides) in functionally relevant ribosome complexes containing A-site aminoacyl-tRNA and
P-site peptidyl-tRNA we will provide atomic-level view of their interactions not only with the ribosome (as before)
but also with the growing peptide. Moreover, such structures could also reveal rearrangements that take place
in the PTC of the ribosome upon drug binding and result in allosteric effects. Hence, in the Specific Aim 1, we
will focus on obtaining the structures of 70S complexes carrying various aminoacyl-tRNAs in the A site in the
presence and absence of CHL. Then, in the Specific Aim 2, we will obtain the first set of CHL-bound ribosome
structures featuring dipeptidyl-tRNAs in the P site containing alanine, serine, or threonine in the penultimate
position (the only sequence requirement for the efficient CHL-induced stalling). Finally, in the Specific Aim 3, we
will provide structural and mechanistic insights into the context-specific activity of ERY and other macrolides.
Once our proposed methodology is established and refined, we will expand it onto the newest FDA-approved
clinically important drugs, such as linezolid, tedizolid, telithromycin, and solithromycin. The anticipated findings
should significantly expand our understanding of the general mode of action of basic, as well as clinically-
important, antibacterial drugs that act upon the catalytic center of the ribosome and may open new venues for...

## Key facts

- **NIH application ID:** 9898395
- **Project number:** 5R01GM132302-02
- **Recipient organization:** UNIVERSITY OF ILLINOIS AT CHICAGO
- **Principal Investigator:** YURY POLIKANOV
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $314,531
- **Award type:** 5
- **Project period:** 2019-04-01 → 2023-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9898395

## Citation

> US National Institutes of Health, RePORTER application 9898395, Molecular mechanisms of action of ribosome-targeting antibiotics. (5R01GM132302-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9898395. Licensed CC0.

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