MD simulations and multivariate studies for modeling the antileishmanial activity of peptides.

Leishmaniasis, a protozoan-caused disease, requires alternative treatments with minimized side-effects and less prone to resistance development. Antimicrobial peptides represent a possible choice to be developed. We report on the prospection of structural parameters of 23 helical antimicrobial and leishmanicidal peptides as a tool for modeling and predicting the activity of new peptides. This investigation is based on molecular dynamic simulations (MD) in mimetic membrane environment, as most of these peptides share the feature of interacting with phospholipid bilayers. To overcome the lack of experimental data on peptides' structures, we started simulations from designed 100% α-helices. This procedure was validated through comparisons with NMR data and the determination of the structure of Decoralin-amide. From physicochemical features and MD results, descriptors were raised and statistically related to the minimum inhibitory concentration against Leishmania by the multivariate data analysis technique. This statistical procedure confirmed five descriptors combined by different loadings in five principal components. The leishmanicidal activity depends on peptides' charge, backbone solvation, volume, and solvent-accessible surface area. The generated model possesses good predictability (q2  = 0.715, r2  = 0.898) and is indicative for the most and the least active peptides. This is a novel theoretical path for structure-activity studies combining computational methods that identify and prioritize the promising peptide candidates.

Role of peptide-peptide interactions in aggregation: Protonectins observed in equilibrium and replica exchange molecular dynamics simulations.

Protonectin (ILGTILGLLKGL-NH2), a peptide extracted from the venom of the wasp Agelaia pallipes pallipes, promotes mast cell degranulation activity, antibiosis against Gram-positive and -negative bacteria, and chemotaxis in polymorphonucleated leukocytes. Another peptide from the same venom, Protonectin (1-6), corresponding to the first six residues of Protonectin, exhibits only chemotaxis. A 1:1 mixture of these two peptides showed positive synergistic antimicrobial effects, attributed to the formation of a heterodimer.16 The antimicrobial activity is probably related to the peptides' interaction with membrane phospholipids. Equilibrium and replica exchange molecular dynamics simulations were used to investigate two systems: the interaction of Protonectins (two molecules) and that of a mixture Protonectin and Protonectin (1-6) in the environment of sodium dodecyl sulfate (SDS) micelles, which mimic bacterial membranes and are also highly anionic. We found that in both systems the peptides tend to aggregate in the aqueous environment and are held together by hydrophobic interactions and hydrogen bonds. In the equilibrium simulations, aggregated Protonectin/Protonectin (1-6) dissociates after penetrating the SDS micelle, whereas the two Protonectins remain associated throughout the simulation time. Also, in the replica exchange simulations, the Protonectins remain closer, associating through a greater number of hydrogen bonds, and were found at only one free energy minimum, whereas the peptides in the mixture display other probable distances from each other, which are significantly longer than those observed with two Protonectin molecules. Coulomb contributions and the free energy of the systems containing micelles were calculated and show that the interactions of the mixed peptides are favored, whereas the interactions between pure Protonectins are more probable. As a consequence of the preferential interaction with the micelle, the Protonectin molecule of the mixed system presents a higher helical structure content. The enhancement of the amphipathic features caused by Protonectin (1-6) can be related to the increase in the antimicrobial activity experimentally observed.

Combining experimental evidence and molecular dynamic simulations to understand the mechanism of action of the antimicrobial octapeptide jelleine-I.

Jelleines are four naturally occurring peptides that comprise approximately eight or nine C-terminal residues in the sequence of the major royal jelly protein 1 precursor (Apis mellifera). The difference between these peptides is limited to one residue in the sequence, but this residue has a significant impact in their efficacy as antimicrobials. In peptide-bilayer experiments, we demonstrated that the lytic, pore-forming activity of Jelleine-I is similar to that of other cationic antimicrobial peptides, which exhibit stronger activity on anionic bilayers. Results from molecular dynamics simulations suggested that the presence of a proline residue at the first position is the underlying reason for the higher efficacy of Jelleine-I compared with the other jelleines. Additionally, simulations suggested that Jelleine-I tends to form aggregates in water and in the presence of mimetic membrane environments. Combined experimental evidence and simulations showed that the protonation of the histidine residue potentiates the interaction with anionic palmitoyl-oleoyl-phosphatidylcholine/palmitoyl-oleoyl-phosphatidylglycerol (POPC/POPG) (70:30) bilayers and reduces the free energy barrier for water passage. The interaction is driven by electrostatic interactions with the headgroup region of the bilayer with some disturbance of the acyl chain region. Our findings point to a mechanism of action by which aggregated Jelleine-I accumulates on the headgroup region of the membrane. Remaining in this form, Jelleine-I could exert pressure to accommodate its polar and nonpolar residues on the amphiphilic environment of the membrane. This pressure could open pores or defects, could disturb the bilayer continuity, and leakage would be observed. The agreement between experimental data and simulations in mimetic membranes suggests that this approach may be a valuable tool to the understanding of the molecular mechanisms of action.