Berberine locks a TMPRSS2 DNA structure linked to viral entry
High-resolution NMR structures reveal how a natural alkaloid recognizes the major G-quadruplex in the TMPRSS2 promoter
image: (A) Coptis chinensis Franch. is rich in berberine, and the surface view of the BER-TMPRSS2-G4 complex structure is shown. (B) 1D 1H NMR spectra displaying imino region changes of TMPRSS2-G4 upon titration with berberine. The top spectrum corresponds to the 35 °C, 3∶1 BER-TMPRSS2-G4 complex. (C) Representative 2D NOESY spectra of the 3∶1 BER-TMPRSS2-G4 complex show intermolecular cross-peaks between berberine and TMPRSS2-G4 at 35 °C. Conditions: 1.93 mmol·L−1 DNA, 350 ms mixing time, 10 mmol·L−1 K+ solution, pH 7.0.
Credit: Chinese Journal of Natural Medicines
TMPRSS2 is a host serine protease that helps influenza viruses and SARS-CoV-2 enter cells, making it an attractive target for antiviral intervention. Rather than blocking the protein after it is produced, one alternative strategy is to suppress TMPRSS2 at the gene-regulatory level. A guanine-rich sequence in the proximal promoter of TMPRSS2 can fold into a G-quadruplex (G4), a non-canonical DNA structure known to influence transcription. Until now, however, the precise architecture of the major TMPRSS2-G4 and its recognition by small molecules had remained unresolved.
In a study published in the Chinese Journal of Natural Medicines, researchers determined the first high-resolution nuclear magnetic resonance solution structure of the major TMPRSS2-G4. The structure adopts a parallel-stranded topology built around a three-tetrad core. Importantly, the 3′ and 5′ flanking regions are not disordered appendages; instead, they form well-defined capping structures stabilized by multiple hydrogen bonds, indicating that these terminal segments are integral to the overall fold.
The study also identified a detailed recognition mode for berberine, a natural alkaloid with reported antiviral properties. The authors found that berberine binds strongly to the major TMPRSS2-G4 and solved the structure of the complex at a 2:1 stoichiometry. One berberine molecule binds at each outer G-tetrad, and in each case, the ligand recruits a neighboring flanking residue to form a coplanar stacking arrangement over the terminal tetrad. This finding provides a concrete structural explanation for how small molecules can achieve selective recognition of promoter G4s through coordinated interactions with both the G-tetrad surface and adjacent flanking nucleotides.
Beyond the isolated structural model, the researchers further showed that the major TMPRSS2-G4 can stably form in a longer DNA context and can be targeted by small molecules to inhibit DNA polymerase activity. These observations support the biological relevance of this promoter element and suggest that stabilizing the TMPRSS2-G4 may be a feasible route to interfere with transcription-associated processes that control TMPRSS2 expression. In this sense, the work does more than describe an unusual DNA fold; it establishes a structure-guided framework for developing antiviral agents that act on a host regulatory element rather than directly on a viral protein.
Taken together, the study provides a structural basis for targeting the major TMPRSS2-G4 with small molecules and identifies berberine as a chemically informative ligand scaffold for future optimization. By clarifying how this DNA structure is organized and recognized, the work may facilitate the design of novel antiviral therapeutics aimed at reducing TMPRSS2-dependent viral entry.