Flavonoids target hidden DNA structures in tuberculosis bacteria

Tuberculosis (TB) remains a major global health challenge, driven by infections with Mycobacterium tuberculosis (Mtb) and complicated by the rise of multi-drug-resistant (MDR) and extensively drug-resistant (XDR) strains. Current treatments often require prolonged use of first- and second-line drugs, which can cause severe side effects and lead to poor patient adherence. Researchers led by Nerges Mistry have focused on an overlooked part of the bacterial genome: non-canonical DNA structures known as G-quadruplexes (GQ) and i-Motifs (iM). These folded forms of DNA are not the familiar double helix, but they can influence how genes are turned on or off and play roles in virulence, stress responses, and mechanisms of drug resistance in Mtb. Flavonoids — naturally occurring polyphenolic compounds found in many fruits and vegetables — have shown promise in other settings for boosting the effect of traditional drugs while reducing toxicity. In this study, Mistry and colleagues set out to test whether two flavonoids, quercetin and kaempferol, can interact with and influence these GQ and iM structures in the Mtb genome, pointing to a fundamentally different way to interfere with the bacterium’s defenses.

To probe these interactions, the team used biophysical tools including UV-Vis absorption spectroscopy, binding constant determination, and thermal melting experiments. They first identified key GQ/iM sequences from Mtb genes associated with drug resistance and then tested how quercetin and kaempferol interacted with those sequences. The exact DNA targets evaluated included cyp51 GQ, dnaB GQ, espB GQ, espE GQ, SigA iM, fabH iM, and psk5 iM. Results showed that quercetin and kaempferol preferentially interact with these specific cyp51 GQ, dnaB GQ, espB GQ, espE GQ, SigA iM, fabH iM, psk5 iM DNA sequences, as indicated by significant changes in absorption spectra. The calculated binding constants demonstrated strong affinities for these particular DNA structures. Thermal melting experiments further indicated that flavonoids increased the thermal stability of these particular GQ and iM DNA, suggesting stabilization via strong stacking interactions between the flavonoids and the folded DNA forms.

These findings point to a new, targeted approach against Mtb that works at the level of DNA architecture rather than conventional drug targets. By stabilizing G-quadruplexes and i-Motifs in genes linked to virulence and drug resistance, quercetin and kaempferol could disrupt the bacterium’s ability to respond to stress and evade treatment. The study highlights flavonoids as promising agents to target GQ/iM DNA structures, offering a new strategy for addressing Mtb drug resistance and virulence. Because flavonoids are common dietary compounds that have shown the ability to enhance traditional TB drugs while minimizing cytotoxicity, this line of research could complement existing therapies and point toward treatments that are more selective and potentially less harmful. While these results come from controlled biophysical experiments, they open the door to further work to determine whether targeting non-canonical DNA structures can be developed into practical therapies for MDR and XDR tuberculosis.