The effect of turn residues on the folding and cell-penetrating activity of β-hairpin peptides and applications toward protein delivery

Deciphering optimal molecular determinants of non-hemolytic, cell-penetrating antimicrobial peptides through bioinformatics and Random Forest

Antimicrobial peptides (AMPs) are promising molecules for combating resistant pathogens, offering several advantages like broad-spectrum effectiveness and multi-targeted action. While most AMPs exhibit membranolytic activity similar to hemolytic peptides (HPs), some act by entering cells like cell-penetrating peptides (CPPs). The toxicity of AMPs towards the host is the major hurdle in their development and application. Given the peptides' function and toxicity largely depend on their molecular properties, identifying and fine-tuning these factors is imperative for developing effective and safe AMPs. To address these knowledge gaps, we present a study that employs a holistic strategy by investigating the molecular descriptors of AMPs, CPPs, HPs, and non-functional equivalents. The prediction of functional properties categorized datasets of 3697 experimentally validated peptides into six groups and three clusters. Predictive and statistical analyses of physicochemical and structural parameters revealed that AMPs have a mean hydrophobic moment of 1.2, a net charge of 4.5, and a lower isoelectric point of 10.9, with balanced hydrophobicity. For cluster AC-nHPs containing peptides with antimicrobial, cell-penetrating, and non-hemolytic properties, disordered conformation and aggregation propensities, followed by amphiphilicity index, isoelectric point, and net charge were identified as the most critical properties. In addition, this work also explains why most AMPs and HPs are membrane-disruptive, while CPPs are non-membranolytic. In conclusion, the study identifies optimal molecular descriptors and offers valuable insights for designing effective, non-toxic AMPs for therapeutic use.

Selection of Nucleotide-Encoded Mass Libraries of Macrocyclic Peptides for Inaccessible Drug Targets

Technological advances and breakthrough developments in the pharmaceutical field are knocking at the door of the "undruggable" fortress with increasing insistence. Notably, the 21st century has seen the emergence of macrocyclic compounds, among which cyclic peptides are of particular interest. This new class of potential drug candidates occupies the vast chemical space between classic small-molecule drugs and larger protein-based therapeutics, such as antibodies. As research advances toward clinical targets that have long been considered inaccessible, macrocyclic peptides are well-suited to tackle these challenges in a post-rule of 5 pharmaceutical landscape. Facilitating their discovery is an arsenal of high-throughput screening methods that exploit massive randomized libraries of genetically encoded compounds. These techniques benefit from the incorporation of non-natural moieties, such as non- proteinogenic amino acids or stabilizing hydrocarbon staples. Exploiting these features for the strategic architectural design of macrocyclic peptides has the potential to tackle challenging targets such as protein-protein interactions, which have long resisted research efforts. This Review summarizes the basic principles and recent developments of the main high-throughput techniques for the discovery of macrocyclic peptides and focuses on their specific deployment for targeting undruggable space. A particular focus is placed on the development of new design guidelines and principles for the cyclization and structural stabilization of cyclic peptides and the resulting success stories achieved against well-known inaccessible drug targets.

Passive Membrane Permeability of Sizable Acyclic β-Hairpin Peptides

The recent shift toward increasingly larger drug modalities has created a significant demand for novel classes of compounds with high membrane permeability that can inhibit intracellular protein-protein interactions (PPIs). While major advances have been made in the design of cell-permeable helices, stapled β-sheets, and cyclic peptides, the development of large acyclic β-hairpins lags far behind. Therefore, we investigated a series of 26 β-hairpins (MW > 1.6 kDa) belonging to a chemical space far beyond the Lipinski "rule of five" (fbRo5) and showed that, in addition to their innate plasticity, the lipophilicity of these peptides (log D 7.4 ≈ 0 ± 0.7) can be tuned to drastically improve the balance between aqueous solubility and passive membrane permeability.

Stapled β-Hairpins Featuring 4-Mercaptoproline

Peptides constrained by intramolecular cross-links, especially stapled α-helices, have emerged as versatile scaffolds for drug development. However, there are fewer examples of similarly constrained scaffolds for other secondary structures. Here, we used a novel computational strategy to identify an optimal staple for antiparallel β-strands, and then we incorporated that staple within a β-hairpin peptide. The hairpin uses 4-mercaptoproline as a novel staple component, which contributes to a unique, kinked structure. The stapled hairpins show a high degree of structure in aqueous solution, excellent resistance to degradation in cell lysates, and cytosolic penetration at micromolar concentrations. They also overlay with a unique subset of kinked hairpin motifs at protein-protein interaction interfaces. Thus, these scaffolds represent promising starting points for developing inhibitors of cellular protein-protein interactions.

Uncoupling the Folding-Function Paradigm of Lytic Peptides to Deliver Impermeable Inhibitors of Intracellular Protein-Protein Interactions

Here, we describe the use of peptide backbone N-methylation as a new strategy to transform membrane-lytic peptides (MLPs) into cytocompatible intracellular delivery vehicles. The ability of lytic peptides to engage with cell membranes has been exploited for drug delivery to carry impermeable cargo into cells, but their inherent toxicity results in narrow therapeutic windows that limit their clinical translation. For most linear MLPs, a prerequisite for membrane activity is their folding at cell surfaces. Modification of their backbone with N-methyl amides inhibits folding, which directly correlates to a reduction in lytic potential but only minimally affects cell entry. We synthesized a library of N-methylated peptides derived from MLPs and conducted structure-activity studies that demonstrated the broad utility of this approach across different secondary structures, including both β-sheet and helix-forming peptides. Our strategy is highlighted by the delivery of a notoriously difficult class of protein-protein interaction inhibitors that displayed on-target activity within cells.