Prediction of SafD adhesin strong binding peptides for pilus proteins assembly suppression in the prevention of Salmonella-induced biofilm formation using virtual mutagenesis studies.

Clinical isolates of Salmonella enterica contain Saf pili that establish initial bacterial attachment with the human epithelium to form biofilms which are a common cause of several abdominal complications. Due to the rise in antibiotic-resistant strains of bacteria, an alternate strategy of inhibiting the initial bacterial contact with the epithelial layers is well-studied. Saf pili undergo a chaperone-usher pathway assembly mechanism to generate its host-recognizing functional form, SafDAA. Preventing the biogenesis of the pili by targeting the SafD and SafA proteins polymerization will prevent host recognition. In this study, virtual mutagenesis studies using the recently reported X-ray crystal structure of an N-terminal peptide co-crystallized with SafD led to the design of peptides that exhibit enhanced binding with SafD compared to its native peptide. Virtual alanine mutagenesis and protein-peptide interaction studies identified several hotspot residues. Molecular dynamics simulations and binding free energy calculations identified key pairwise interactions between the designed peptides and SafD. In addition, a library of 110 peptides that are predicted to bind strongly with SafD is prepared which can serve as an excellent resource for the discovery of novel SafD-binding peptides. This work provided new insights into the design of novel anti-virulence therapies targeting Salmonella enterica.

Supplementary information: The online version contains supplementary material available at 10.1007/s40203-025-00313-9.