Bypassing the Need for Cell Permeabilization: Nanobody CDR3 Peptide Improves Binding on Living Bacteria

Abstract

Membrane interaction constitutes to be an essential parameter in the mode of action of entities such as proteins, as well as cell-penetrating and antimicrobial peptides, resulting in noninvasive or lytic activities depending on the membrane compositions and interactions. Recently, a nanobody able to interact with the top priority, multidrug-resistant bacterial pathogen Acinetobacter baumannii was discovered, although binding took place with fixed cells only. To potentially overcome this limitation, linear peptides corresponding to the complementarity-determining regions (CDR) were synthesized and fluorescently labeled. Microscopy data indicated clear membrane interactions of the CDR3 sequence with living A. baumannii cells, indicating both the importance of the CDR3 as part of the parent nanobody paratope and the improved binding ability and thus avoiding the need for permeabilization of the cells. In addition, cyclization of the peptide with an additionally introduced rigidifying 1,2,3-triazole bridge retains its binding ability while proteolytically protecting the peptide. Overall, this study resulted in the discovery of novel peptides binding a multidrug-resistant pathogen.

Cryo-EM structures of type IV pili complexed with nanobodies reveal immune escape mechanisms

“…The design of multi-specific nanobody or nanobody-like constructs with Fc-mimicking domains is indeed possible, as evidenced by recent developments in the drug-design field such as TriTACs 26 or DARPins 27 . Short, synthetic peptide-mimetics based on the CDR sequences can also be explored 28 . Overall, our work opens new avenues of research and show promise to use type IV pili as diagnostic and therapeutic tools for these deadly infections.…”

Nano-based theranostic approaches for infection control: current status and perspectives

“…73,74 Binding peptides with smaller sizes than antibodies exhibit higher stability at diverse pH levels, 75 while the peptide cyclization into the nanobody forms can further improve their proteolytic stability. 76…”

“…73,74 Binding peptides with smaller sizes than antibodies exhibit higher stability at diverse pH levels, 75 while the peptide cyclization into the nanobody forms can further improve their proteolytic stability. 76 Similar to antibodies, aptamers not only have excellent specificity and affinity to cellular targets but also possess key advantages, including high stability, low cost and flexibility to incorporate chemical modification for modulating the binding affinity. The selection of deoxyribonucleic acid (DNA) aptamers against bacterial cells can be achieved by an in vitro process known as the systematic evolution of ligands by exponential enrichment (SELEX).…”