Researchers have identified a previously hidden motion in RNA polymerase (RNAP) that is essential for transcribing DNA into RNA and shown how two experimental antibiotics block that motion to stop gene expression. The work, published in the Proceedings of the National Academy of Sciences in 2026, comes from the Darst laboratory at Rockefeller University and sheds light on both a fundamental step in biology and a mechanism that could be exploited for new antimicrobials.
What the researchers found
The team used the antibiotics as molecular probes to reveal that RNAP requires a brief conformational movement — a mobile structural element swinging into place — to stabilise RNA synthesis. When that movement is prevented, the enzyme cannot sustain transcription and gene expression grinds to a halt. Two experimental compounds, CBR9379 (active on Escherichia coli RNAP) and AAP‑SO2 (active on Mycobacterium tuberculosis RNAP), achieve inhibition by binding and effectively locking this mobile element so it cannot adopt the position needed for productive RNA synthesis.
“It’s sort of a two‑for‑one,” said Seth A. Darst of the Laboratory of Molecular Biophysics at Rockefeller. “We now know how these inhibitors work, and the inhibitors also revealed a conformational change in the active site that we didn’t know was important.”
The report emphasises that earlier structural methods, such as traditional X‑ray crystallography, are excellent at capturing static snapshots of proteins but had been unable to resolve the dynamic motion that proves critical in this case. By leveraging the antibiotics as tools, the researchers could infer and capture functionally relevant states of RNAP that had been obscure until now.
Why this matters
RNA polymerase is the molecular machine that copies DNA into RNA — a step central to gene expression in all cells. Discovering a conserved, previously unrecognised conformational requirement for RNAP activity has two immediate consequences.
- Fundamental biology: it identifies a conserved mechanistic step in transcription across diverse forms of life, refining our understanding of how genetic information is transcribed.
- Antibiotic development: it defines a targetable movement within RNAP that new drugs could exploit, offering a blueprint for designing molecules that lock the enzyme in an inactive conformation.
The study therefore functions both as a mechanistic advance and as a proof of principle that small molecules can be designed to arrest essential molecular motions in an enzyme central to cell viability.
Details at a glance
| Compound | Target organism RNAP | Action |
|---|---|---|
| CBR9379 | E. coli RNAP | Locks a mobile active‑site element, preventing the conformational change needed for RNA synthesis |
| AAP‑SO2 | M. tuberculosis RNAP | Similarly prevents the mobile element from adopting the active conformation, inhibiting transcription |
Limitations and next steps
The findings are grounded in structural and biochemical analysis reported in PNAS (DOI: 10.1073/pnas.2609228123). As the authors note, these are experimental antibiotic classes rather than approved medicines; additional work will be necessary to evaluate toxicity, spectrum of activity, propensity for resistance, and suitability for clinical development. The study does not yet provide a fully characterised drug candidate, but it lays out a specific structural vulnerability of RNAP that medicinal chemists can target.
For countries facing a heavy burden of drug‑resistant infections, including South Africa with a high tuberculosis caseload, new mechanisms that can be exploited to produce antibiotics are especially important. A drug that targets a conserved mechanical step in RNAP could, in principle, be developed to have potent activity against difficult pathogens, although that path remains long and requires careful preclinical and clinical evaluation.
Concluding perspective
This work is an example of how using inhibitors as investigative tools can reveal otherwise hidden aspects of molecular machines. By demonstrating that two chemically distinct compounds immobilise a crucial RNAP motion, the study both clarifies how these inhibitors work and opens a clearer route for rational drug design centred on enzyme dynamics rather than only static binding pockets.
The discovery underlines a broader lesson for antibiotic discovery: understanding the dynamics of essential bacterial enzymes provides fresh opportunities to develop drugs that act by freezing critical motions rather than merely occupying active sites.
