Influence of Different Aromatic Hydrophobic Residues on the Antimicrobial Activity and Membrane Selectivity of BRBR-NH₂ Tetrapeptide

Abstract

The ultrashort linear antimicrobial tetrapeptide BRBR-NH 2 with an unnatural residue biphenylalanine (B) has potent and rapid antimethicillin-resistant Staphylococcus aureus (MRSA) activity but lacks hemolytic activity. The anti-MRSA activity of BRBR-NH 2 is 8-fold more potent than that of WRWR-NH 2 and 16-fold more potent than that of FRFR-NH 2 . However, how to influence their antimicrobial activities and mechanisms through the substitution of different aromatic hydrophobic residues is still unclear. In this work, to study the effects of varying hydrophobic interactions and membrane selectivities of BRBR-NH 2 , we performed multiple long-time (1000 ns) molecular dynamics (MD) simulations to investigate the interactions of a red blood cell (RBC) membrane and a Gram-positive bacterial cell membrane with three different tetrapeptides (BRBR-NH 2 , WRWR-NH 2 , and FRFR-NH 2 ) under different ratios of peptides and lipids and also explored the changes in the membrane and structural characteristics of peptides. The binding energy results show that BRBR-NH 2 interacts weakly with the RBC membrane, while not all BRBR-NH 2 can be adsorbed to the RBC membrane surface. The MD simulation results produced significant local membrane thinning of multiBRBR-NH 2 peptides in the Gram-positive bacterial cell membrane. An in-depth analysis of structural features and peptide−membrane interactions suggests that the aggregation of BRBR-NH 2 on the membrane surface plays a crucial role in the destruction of the cell membrane. Taken together with the observed local membrane thinning, the in-depth analysis demonstrated that the interactions between the lipid bilayer and the BRBR-NH 2 aggregation surface result in a local disturbance of the membrane structure. It can be concluded that the high anti-MRSA activity of BRBR-NH 2 is attributed to the aggregation of BRBR-NH 2 on the membrane surface. On the other hand, WRWR-NH 2 and FRFR-NH 2 peptides tend to bind with the membrane surface in a monomeric form and cover the membrane surface in a carpet-like manner. Therefore, these results provide an advanced microscopic understanding of how hydrophobic interactions or hydrophobic residues affect the antimicrobial activity and mechanism of antimicrobial peptides (AMPs).

Peptide Power: Mechanistic Insights into the Effect of Mitochondria-Targeted Tetrapeptides on Membrane Electrostatics from Molecular Simulations

“…The research group studying UsAMPs further found that increasing the hydrophobicity of their aromatic residues, from Phe to Trp to an engineered biphenylalanine, led to deeper penetration into the hydrophobic core, stronger membrane thinning, increased membrane disruption, and more potent anti-MRSA activity. , This suggests that some of MTP’s less hydrophobic aromatic residues (like Phe in SS-20) or more strongly hydrophobic aromatic residues with hydrogen bonding capacities (like Dmt in SS-31 or Trp in SPN10) may represent an optimal design for MTPs because they do not bury as deeply into the bilayer as UsAMPs. The shallower insertion depth of MTPs may be sufficient to cause a meaningful change in the C m without causing such acute membrane thinning that the bilayer becomes vulnerable to disruption.…”

“…Like MTPs, most AMPs are amphipathic and strongly cationic; unlike MTPs, AMPs exert their MoA by disrupting membranes and inducing bacterial cell lysis. − It is worth noting that AMP (and other related small peptide)–membrane interactions have been heavily studied using MD simulations. − Of particular relevance is a family of synthetic ultrashort antimicrobial tetrapeptides (UsAMPs) for methicillin-resistant Staphylococcus aureus (MRSA) infections. These peptides share the same alternating cationic–aromatic sequence motif as MTPs − but have two arginines instead of an arginine and a lysine. They found that replacing arginines with lysines nullified the UsAMPs’ anti-MRSA activity, possibly because arginines mediate rapid binding to negatively charged bilayers and their planar gaunidinium group can coordinate multiple lipid phosphates, potentially leading to increased bilayer defects. ,, This suggests that the Arg–Lys pair in MTPs may be optimal because it can weakly coordinate anionic lipids such as TOCL and alter membrane electrostatics without disrupting membranes such as the UsAMPs.…”

The Design of Alapropoginine, a Novel Conjugated Ultrashort Antimicrobial Peptide with Potent Synergistic Antimicrobial Activity in Combination with Conventional Antibiotics

“…Alapropoginine was also conjugated to a carbon side chain composed of 2-(6-methoxynaphthalen-2-yl)propanoic acid. The rationale behind the conjugation strategy is to sustain the hydrophobic grip of the biphenylalanine amino acids and provide a hydrophobic stabilizer to the peptide [33].…”

Effects of C-Terminal Lys-Arg Residue of AapA1 Protein on Toxicity and Structural Mechanism

“…Molecular dynamics (MD) simulations in conjunction with enhanced sampling method provide an effective tool for revealing protein–membrane interactions at the atomistic level and complementing experimental results [ 6 , 7 , 8 , 9 ]. The first category of studies [ 4 , 10 , 11 , 12 , 13 , 14 , 15 ] typically involves placing monomeric or oligomeric toxin proteins/antibacterial peptides either on the surface of bilayer membrane or directly in a transmembrane helical state, with a focus on investigating local structural characteristics such as changes in membrane properties and peptide conformations via conventional molecular dynamics (CMD) simulations. Steinbrecher et al [ 10 ] studied the protein–lipid interaction and structures of monomeric, dimeric, and oligomeric TisB toxin proteins by using coarse-grained MD simulation.…”