With the development of de novo binders for
protein targets from non-related scaffolds, many possibilities for
therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC
protein.
Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid
typhoid diagnostics will improve disease management and
therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC
protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied"
amino acid residues against TolC surface. Next, scFv scaffolds were selected from
Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold
complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural
protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of
antigen-based detection agents for
typhoid diagnostics.