Fast and potent bactericidal membrane lytic activity of PaDBS1R1, a novel cationic antimicrobial peptide

© 2018 Elsevier B.V. All rights reserved.
Antimicrobial peptides (AMPs) are promising candidates for the development of future antibiotics. In an attempt to increase the efficacy of therapeutic AMPs, computer-based design methods appear as a reliable strategy. In this study, we evaluated the antimicrobial efficiency and mechanism of action of a novel designed AMP named PaDBS1R1, previously designed by means of the Joker algorithm, using a fragment of the ribosomal protein L39E from the archaeon Pyrobaculum aerophilum as a template. PaDBS1R1 displayed low micromolar broad-spectrum antimicrobial activity against Gram-negative (MIC of 1.5 μM) and Gram-positive (MIC of 3 μM) bacteria, including carbapenem-resistant Klebsiella pneumoniae (MIC of 6.25 μM) and methicillin-resistant Staphylococcus aureus (MIC of 12.5 μM), without cytotoxicity towards HEK-293 cells. In addition, membrane permeabilization and depolarization assays, combined with time-kill studies and FEG-SEM imaging, indicated a fast membrane permeation and further leakage of intracellular content. Biophysical studies with lipid vesicles show a preference of PaDBS1R1 for Gram-negative bacteria-like membranes. We investigated the three-dimensional structure of PaDBS1R1 by CD and NMR analyses. Our results suggest that PaDBS1R1 adopts an amphipathic α-helix upon interacting with hydrophobic environments, after an initial electrostatic interaction with negative charges, suggesting a membrane lytic effect. This study reveals that PaDBS1R1 has potential application in antibiotic therapy.
The authors acknowledge Fundação para a Ciência e a Tecnologia – Ministério da Ciência, Tecnologia e Ensino Superior (FCT-MCTES, Portugal) for funding, including fellowship SFRH/BD/100517/2014 to M.R.F., Marie Sklodowska-Curie Research and Innovation Staff Exchange (MSCA-RISE, European Union) project INPACT (call H2020-MSCA-RISE-2014, grant agreement 644167), IMPC (Institut des Matériaux de Paris Centre, FR 2482) and the C'Nano projects of the Region Ile-de-France for SEM-FEG funding. Conselho Nacional de Desenvolvimento Científico e Tecnológico – CNPq for financial support and researcher fellowship (Processes: 141327/2012-0; 407181/2013-0; 303181/20150), Coordenação de Aperfeiçoamento de Pessoal do Nível Superior – CAPES, for scholarship (Process: BEX 2758/15-6), and Fundação de Amparo à Pesquisa do Estado de Goiás – FAPEG (Process: 201710267000062). This work was also supported by Fundação de Amparo a Pesquisa do Mato Grosso do Sul (FUNDECT) and Fundação de Amapro a Pesquisa do Distrito Federal (FAPDF).