Engineering Antimicrobial Peptides with Improved Antimicrobial and Hemolytic Activities

Abstract

The rapid rise of antibiotic resistance in pathogens becomes a serious and growing threat to medicine and public health. Naturally occurring antimicrobial peptides (AMPs) are an important line of defense in the immune system against invading bacteria and microbial infection. In this work, we present a combined computational and experimental study of the biological activity and membrane interaction of the computationally designed Bac2A-based peptide library. We used the MARTINI coarse-grained molecular dynamics with adaptive biasing force method and the umbrella sampling technique to investigate the translocation of a total of 91 peptides with different amino acid substitutions through a mixed anionic POPE/POPG (3:1) bilayer and a neutral POPC bilayer, which mimic the bacterial inner membrane and the human red blood cell (hRBC) membrane, respectively. Potential of mean force (PMF, free energy profile) was obtained to measure the free energy barrier required to transfer the peptides from the bulk water phase to the water-membrane interface and to the bilayer interior. Different PMF profiles can indeed identify different membrane insertion scenarios by mapping out peptide-lipid energy landscapes, which are correlated with antimicrobial activity and hemolytic activity. Computationally designed peptides were further tested experimentally for their antimicrobial and hemolytic activities using bacteria growth inhibition assay and hemolysis assay. Comparison of PMF data with cell assay results reveals a good correlation of the peptides between predictive transmembrane activity and antimicrobial/hemolytic activity. Moreover, the most active mutants with the balanced substitutions of positively charged Arg and hydrophobic Trp residues at specific positions were discovered to achieve the improved antimicrobial activity while minimizing red blood cell lysis. Such substitutions provide more effective and cooperative interactions to distinguish the peptide interaction with different lipid bilayers. This work provides a useful computational tool to better understand the mechanism and energetics of membrane insertion of AMPs and to rationally design more effective AMPs.

Conjugation of Aurein 2.2 to HPG Yields an Antimicrobial with Better Properties

“…Thus we tested the interaction of HPG conjugates with various blood components by measuring the red cell lysis, platelet aggregation and activation, complement activation and blood coagulation.Previous studies have demonstrated that the toxicity of the AMPs can be correlated with their ability to lyse red blood cells. Recently, Zhao et al72 used a computational approach to develop peptides with improved antimicrobial activity while minimizing red blood cell lysis. To study the interaction of conjugates with RBCs, washed RBCs were incubated with the conjugates at 37 °C and the percent lysis was measured.…”

The dimerization of PSGL‐1 is driven by the transmembrane domain via a leucine zipper motif

“…The PMF calculation method provides a view of the free energy landscape to predict and analyze the helix‐helix interactions of the TMD dimer in a lipid bilayer, and it has been confirmed that the free energies of dimerizaition in the CG model are similar to those from more detailed all‐atom simulations . Furthermore, the all‐atom simulation models can refine the atomistic structure of the dimers and provide a more detailed description of the underlying peptide–peptide interactions …”

Nanoparticles Suitable for BCAA Isolation Can Serve for Use in Magnetic Lipoplex-Based Delivery System for L, I, V, or R-rich Antimicrobial Peptides

“…Furthermore, it was found that binding of peptides slightly elevates the entire complex size distribution and zeta potential, when compared to binding of single amino acids. An increase of zeta potential to a more positive value is considered as beneficial because the cationic nature of the peptide enhances the specificity of their binding to bacterial cell membranes relative to human cell membranes, because the former contain a greater amount of anionic lipids on the outer leaflet [33]. …”