Structure and Modeling of Knottins, a Promising Molecular Scaffold for Drug Discovery

The knottins are extremely stable miniproteins present in many species and are able to perform various tasks. Owing to its small size and its amazing stability, the knottin structural domain is considered as an excellent scaffold for drug development. Several recent databases and web servers dedicated to or aware of knottins have appeared and are shortly described. Altogether they provide a valuable ensemble of data and of specific tools that greatly facilitate knottin-based studies. The essential structural features of the knottin scaffold, which heavily rest on the three knotted disulfide bridges for its stability, are reviewed. These include small but well-conserved secondary structures and hydrogen bonding networks, but also several further interactions that have been shown to be essential for stability and/or activity. Examples are supplementary disulfide bridges, side chain hydrogen bonds, or circularization. General structure prediction and modeling tools are not well fitted to knottins, and several specific tools have been developed. Specifically, methods to assign a disulfide connectivity pattern to small disulfide-rich sequences or to build accurate 3D models of knottins are available and are discussed in the review. Although more works are still needed to better understand sequence-structure-function relationships, recent studies strongly suggest that existing applications of knottins as drugs (i.e. painkillers), molecules for diagnosis, or insecticidal crop treatment should rapidly generalize and extend to other fields as well, e.g. as antimicrobials.