Clostridioides difficile (C. diff) is a gram-positive bacterium which is a serious public health issue often associated with disruption of the gut microbiome. The primary virulence factor of C. diff is Toxin B (TcdB), which causes severe colitis. In this study we developed a computational method to design α-helical peptides to bind to TcdB and block/inhibit its activity. We focused on two distinct classes of peptide inhibitors to disrupt various functions of TcdB. The first group of peptide inhibitors are 30-mer α-helical peptides designed to bind directly to the glucosyltransferase domain (GTD) of TcdB1. The GTD is responsible for modifying host cell proteins and leads to cell death. The peptides in this work are designed to inhibit the GTD’s activity. The second group of peptide inhibitors are 20-mer α-helical peptides designed to block TcdB1 from entering host cells. These peptides bind to the delivery domain of TcdB1 where frizzled proteins normally bind, thus preventing TcdB from getting into cells. The peptides in both cases were designed by modifying our existing Monte Carlo–based Peptide Binding Design algorithm (PepBD). Alpha-helical peptides were designed by incorporating AGADIR, an algorithm based on helix-to-coil transition theory that predicts the α-helical propensity of peptides. The designed peptides were then evaluated with explicit-solvent molecular dynamics simulations to calculate their binding affinity. Parallel-bias well-tempered metadynamics was used to show that our designed peptides adopt the intended α-helical conformations. This computational approach broadens the range of peptides that we can design using PepBD and may pave the way for the rational design of α-helical peptides for a variety of applications.
