Host Defence Peptides (HDPs): investigating the structure-to-function relationship through bio-physical techniques

During last decades, more and more microorganisms resistant to conventional antibiotics were isolated while few new antimicrobial drugs were developed. The urgent need for novel efficient antibiotics led a great attention on cationic host defense peptides (HDP) since their discovery in 1980s. The role of these molecules in the defense of organism against pathogens attack, together with their high selectivity for bacterial cells over the eukaryotic ones, made them attractive candidates for the development of a new class of antimicrobial drugs. At present, a vast range of both natural and synthetic HDPs sequences are reported in the literature but they still present remarkable limitations to an effective applicability in vivo, such as the high sensitivity to proteases and strong activity reduction in the presence of physiological electrolytes concentration. A lot of effort have been put into improving their pharmacokinetics in order to develop new antimicrobial drugs based on their sequences. The present Ph.D. work is focused on the elucidation of the structure-to-function relationships of three different peptides, chosen as representative of different HDP categories. Esculentin-1b(1-18) is the ‘classic’ natural antimicrobial peptide (AMP), Plasticin-L1, is an immunomodulatory peptide devoid of direct bactericidal activity, and a group of four synthetic peptide analogues based on a semi-synthetic dendrimeric and lipidated peptide called SB056. The latter, in particular, represent an innovative class of peptides, whose structural features, three-dimensional folding and mode of action are absolutely peculiar and almost completely unknown before this project started. The interesting and multidisciplinary field of HDPs is presented in the first chapter. The origins, the structural features and the modes of action proposed for these compounds in the literature are briefly summarized. A brief excursus on the limits of their applicability in the clinical practice and the strategies adopted to overcome this issue is also included. In the second chapter, all the materials, the methods and experimental protocols are described, going from typical biological assays to biophysical methods.. The main technique used to elucidate the three-dimensional structure of the peptides, the nuclear magnetic resonance (NMR), is described in more detail. The computational tools used in concert with the NMR data are also described. The chapters 3, 4 and 5 are devoted to the results and discussion of the studies performed on the three aforementioned peptides. Esculentin-1b(1-18) is the 18-mer Nterminal fragment of the peptide esculentin-1b, which was isolated from the granular skin secretions of the European frog Pelophylax lessonae/ridibundus. It is presented in the Chapter 3. The next chapter is dedicated to the studies performed on Plasticin-L1, a 25 amino acid residue peptide isolated from the skin secretions of the South-American Santa Fe frog Leptodactylus laticeps (Leptodactylidae). In Chapter 5 the extensive and challenging work on the four SB056 analogs is reported. Among various scientific collaborations, it has to be emphasized that part of the study on the SB056 peptides was performed in the prof. A.S. Ulrich’s labs at the Karlsruhe Institute of Technology, Germany, where I personally spent a 6 months stage. Finally, in the last chapter, which is devoted to the main conclusions, a general overview of the results is given, highlighting the advance gained in the field of the HDPs and presenting possible outlooks for further peptides improvement