Simulation Study of the Effect of Antimicrobial Peptide Associations on the Mechanism of Action with Bacterial and Eukaryotic Membranes

Improving the antimicrobial potential of the peptide CIDEM-501 through acylation: A computational approach

Acylation is a common method used to modify antimicrobial peptides to enhance their effectiveness. It increases the interactions between the peptide and the bacterial cell membranes. However, acylation can also reduce the selectivity of the peptides by making them more active on eukaryotic membranes, which can lead to unintended toxicity. This study examines the potential of using in silico tools to evaluate the interaction and selectivity of the antimicrobial peptide CIDEM-501 when acylated with decanoic acid at the N-terminus, compared to the non-acylated counterpart. Circular dichroism, microdilution, and hemolysis assays were used to determine the peptide's secondary structure, antimicrobial activity, and selectivity to validate the theoretical predictions. The acylated peptide showed a more stable interaction with the bacterial membrane by inserting the acyl chain into the membrane's hydrophobic core, which led to tighter adsorption and a greater buried surface area. Additionally, it significantly altered membrane order more than the non-acylated counterpart, suggesting superior antimicrobial potential. Finally, in vitro activity assays confirmed theoretical predictions, showing that the acylated peptide had lower Minimum Inhibitory Concentration (MIC) values than the non-acylated peptide. Neither peptide showed significant hemolytic activity at their MIC. The computational techniques used in this study displayed strong predictive capability and helped to elucidate the interaction between the peptide and the membranes.

A novel synthetic peptide analog enhanced antibacterial activity of the frog-derived skin peptide wuchuanin-A1

In recent years, there has been a growing focus on the development of novel antibacterial compounds for clinical applications, such as antimicrobial peptide (AMP). Among the developed AMP, wuchuanin-A1, a coil-shaped bioactive peptide derived from Odorrana wuchuanensis frog skin, has been reported to exhibit antibacterial, antifungal, and antioxidant activity, but there are limited studies on its potential as an antibacterial agent. Therefore, this study aims to molecularly modify the sequence of wuchuanin-A1 to enhance its antibacterial properties. The interaction of both the native and analog peptide with bacterial inner membranes was initially assessed using computational methods. Specific amino acid substitutions were then used to enhance the modified peptide's antibacterial efficacy, followed by several preliminary tests to evaluate its activity. This study bridges the gap in exploring the potential of wuchuanin-A1 for antibacterial purposes, providing insights into the design of effective antimicrobial agents.Communicated by Ramaswamy H. Sarma.

Role of Peptide Associations in Enhancing the Antimicrobial Activity of Adepantins: Comparative Molecular Dynamics Simulations and Design Assessments

Adepantins are peptides designed to optimize antimicrobial biological activity through the choice of specific amino acid residues, resulting in helical and amphipathic structures. This paper focuses on revealing the atomistic details of the mechanism of action of Adepantins and aligning design concepts with peptide behavior through simulation results. Notably, Adepantin-1a exhibits a broad spectrum of activity against both Gram-positive and Gram-negative bacteria, while Adepantin-1 has a narrow spectrum of activity against Gram-negative bacteria. The simulation results showed that one of the main differences is the extent of aggregation. Both peptides exhibit a strong tendency to cluster due to the amphipathicity embedded during design process. However, the more potent Adepantin-1a forms smaller aggregates than Adepantin-1, confirming the idea that the optimal aggregations, not the strongest aggregations, favor activity. Additionally, we show that incorporation of the cell penetration region affects the mechanisms of action of Adepantin-1a and promotes stronger binding to anionic and neutral membranes.

In Silico Study of the Early Stages of Aggregation of β-Sheet Forming Antimicrobial Peptide GL13K

Antimicrobial peptides (AMPs) are of growing interest as potential candidates that may offer more resilience against antimicrobial resistance than traditional antibiotic agents. In this article, we perform the first in silico study of the synthetic ß sheet-forming AMP GL13K. Through atomistic simulations of single and multi-peptide systems under different conditions, we are able to shine a light on the short timescales of early aggregation. We find that isolated peptide conformations are primarily dictated by sequence rather than charge, whereas changing charge has a significant impact on the conformational free energy landscape of multi-peptide systems. We demonstrate that the loss of charge-charge repulsion is a sufficient minimal model for experimentally observed aggregation. Overall, our work explores the molecular biophysical underpinnings of the first stages of aggregation of a unique AMP, laying necessary groundwork for its further development as an antibiotic candidate.

Structure of the Bacterial Cell Envelope and Interactions with Antimicrobials: Insights from Molecular Dynamics Simulations

Bacteria have evolved over 3 billion years, shaping our intrinsic and symbiotic coexistence with these single-celled organisms. With rising populations of drug-resistant strains, the search for novel antimicrobials is an ongoing area of research. Advances in high-performance computing platforms have led to a variety of molecular dynamics simulation strategies to study the interactions of antimicrobial molecules with different compartments of the bacterial cell envelope of both Gram-positive and Gram-negative species. In this review, we begin with a detailed description of the structural aspects of the bacterial cell envelope. Simulations concerned with the transport and associated free energy of small molecules and ions through the outer membrane, peptidoglycan, inner membrane and outer membrane porins are discussed. Since surfactants are widely used as antimicrobials, a section is devoted to the interactions of surfactants with the cell wall and inner membranes. The review ends with a discussion on antimicrobial peptides and the insights gained from the molecular simulations on the free energy of translocation. Challenges involved in developing accurate molecular models and coarse-grained strategies that provide a trade-off between atomic details with a gain in sampling time are highlighted. The need for efficient sampling strategies to obtain accurate free energies of translocation is also discussed. Molecular dynamics simulations have evolved as a powerful tool that can potentially be used to design and develop novel antimicrobials and strategies to effectively treat bacterial infections.

Hyper Thermostability and Liquid-Crystal-Like Properties of Designed α-Helical Peptide Nanofibers

Structural and thermodynamic transitions of artificially designed α-helical nanofibers were investigated using eight peptide variants, including four peptides with amide-modified carboxyl termini (CB peptides) and four unmodified peptides (CF peptides). Temperature-dependent circular dichroism spectroscopy and differential scanning calorimetry showed that CB peptides exhibit thermostability up to 50 °C higher than CF peptides. As a result, one of the denaturation temperatures approached nearly 130 °C, which is exceptionally high for a biomacromolecule. Thermodynamic analysis and microscopy observations also showed that CB peptides undergo a thermal transition similar to the phase transition in liquid crystals. In addition, one of the peptides showed a sharp and highly cooperative transition with a small enthalpy change at around 25 °C, which was ascribed to a giga-bundle burst of the molecular assembly. These macroscopic changes in the thermostability and crystallinity of CB peptides may be attributed to an increased amphiphilicity of the molecule in the direction of the helix axis, originating from the microscopic modification of the carboxyl-terminus.