Virtual Screening\nUncovers DspS Activators That Disperse Pseudomonas\naeruginosa Biofilms

Pseudomonas aeruginosa is the predominant\nbacterium found in many chronic biofilm infections. Over the past\nfew decades, biofilm-related infections have posed a significant challenge\nto medical practice due to the increasing emergence of multidrug resistance. <i>Cis</i>-2-decenoic acid (CDA), a small molecule found in P. aeruginosa, has been shown to disperse biofilms\nformed by various bacteria and to work in synergy with common antibiotics.\nDespite that, the binding mechanism between CDA and the predicted\ncyclases/histidine kinases associated sensory extracellular (CHASE)\ndomain of sensor protein DspS remains unknown in the absence of a\ncrystallized protein structure. Moreover, the therapeutic potential\nof CDA is limited by its susceptibility to oxidative degradation and\nisomerization. In this work, we propose a structural model for the\nDspS CHASE domain. The resulting model displays an overall topology\nreminiscent of the sensor protein PcrK in Xanthomonas\ncampestris. Through molecular dynamics simulations,\na stable potential binding site for CDA was further identified. Virtual\nscreening against the predicted site of DspS CHASE using our developed\npipeline discovered two promising compounds, compounds <b>2</b> and <b>9</b>, capable of dislodging 7-day P.\naeruginosa biofilms at 50 μM without affecting\nbacterial growth. These compounds also enhanced the effects of ciprofloxacin\nagainst P. aeruginosa, reduced the\nsurvival of dispersed cells, and increased the expression of matrix-degrading\nenzyme genes <i>pelA</i>, <i>pslG</i>, and <i>eddA</i>. This study provides insights into CDA recognition\nby DspS and represents the first large-scale effort to uncover first-in-class\nDspS activators. At the same time, this work also underscores the\neffectiveness of a computational-aided drug discovery process in finding\nnew activators, even without a known protein structure.