Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity

Catalytic peptide-based coacervates for enhanced function through structural organization and substrate specificity

Liquid-liquid phase separation (LLPS) in living cells provides innovative pathways for synthetic compartmentalized catalytic systems. While LLPS has been explored for enhancing enzyme catalysis, its potential application to catalytic peptides remains unexplored. Here, we demonstrate the use of coacervation, a key LLPS feature, to constrain the conformational flexibility of catalytic peptides, resulting in structured domains that enhance peptide catalysis. Using the flexible catalytic peptide P7 as a model, we induce reversible biomolecular coacervates with structured peptide domains proficient in hydrolyzing phosphate ester molecules and selectively sequestering phosphorylated proteins. Remarkably, these coacervate-based microreactors exhibit a 15,000-fold increase in catalytic efficiency compared to soluble peptides. Our findings highlight the potential of a single peptide to induce coacervate formation, selectively recruit substrates, and mediate catalysis, enabling a simple design for low-complexity, single peptide-based compartments with broad implications. Moreover, LLPS emerges as a fundamental mechanism in the evolution of chemical functions, effectively managing conformational heterogeneity in short peptides and providing valuable insights into the evolution of enzyme activity and catalysis in prebiotic chemistry.

Determining the esterase activity of peptides and peptide assemblies

Catalytic peptides are gaining attention as alternatives to enzymes, especially in industrial applications. Recent advances in peptide design have improved their catalytic efficiency with approaches such as self-assembly and metal ion complexation. However, the fundamental principles governing peptide catalysis at the sequence level are still being explored. Ester hydrolysis, a well-studied reaction, serves as a widely employed method to evaluate the catalytic potential of peptides. The standard colorimetric reaction involving para-nitrophenyl acetate hydrolysis acts as a benchmark assay, providing a straightforward and efficient screening method for rapidly identifying potential catalysts. However, maintaining standardized conditions is crucial for reproducible results, given that factors such as pH, temperature, and substrate concentration can introduce unwanted variability. This necessity becomes particularly pronounced when working with peptides, which often exhibit slower reaction rates compared to enzymes, making even minor variations significantly influential on the final outcome. In this context, we present a refined protocol for assessing the catalytic activity of peptides and peptide assemblies, addressing critical considerations for reproducibility and accuracy.

Manually curated dataset of catalytic peptides for ester hydrolysis

Catalytic peptides are low cost biomolecules able to catalyse chemical reactions such as ester hydrolysis. This dataset provides a list of catalytic peptides currently reported in literature. Several parameters were evaluated, including sequence length, composition, net charge, isoelectric point, hydrophobicity, self-assembly propensity and mechanism of catalysis. Along with the analysis of physico-chemical properties, the SMILES representation for each sequence was generated to provide an easy-to-use means of training machine learning models. This offers a unique opportunity for the development and validation of proof-of-concept predictive models. Being a reliable manually curated dataset, it also enables the benchmark for comparison of new models or models trained on automatically gathered peptide-oriented datasets. Moreover, the dataset provides an insight in the currently developed catalytic mechanisms and can be used as the foundation for the development of next-generation peptide-based catalysts.

Amino acid containing amphiphilic hydrogelators with antibacterial and antiparasitic activities

Nanoscale self-assembly of peptide constructs represents a promising means to present bioactive motifs to develop new functional materials. Here, we present a series of peptide amphiphiles which form hydrogels based on β-sheet nanofibril networks, several of which have very promising anti-microbial and anti-parasitic activities, in particular against multiple strains of Leishmania including drug-resistant ones. Aromatic amino acid based amphiphilic supramolecular gelators C₁₄-Phe-CONH-(CH₂)_n-NH₂ (n = 6 for P1 and n = 2 for P3) and C₁₄-Trp-CONH-(CH₂)_n-NH₂ (n = 6 for P2 and n = 2 for P4) have been synthesized and characterized, and their self-assembly and gelation behaviour have been investigated in the presence of ultrapure water (P1, P2, and P4) or 2% DMSO(v/v) in ultrapure water (P3). The rheological, morphological and structural properties of the gels have been comprehensively examined. The amphiphilic gelators (P1 and P3) were found to be active against both Gram-positive bacteria B. subtilis and Gram-negative bacteria E. coli and P. aeruginosa. Interestingly, amphiphiles P1 and P3 containing an L-phenylalanine residue show both antibacterial and antiparasitic activities. Herein, we report that synthetic amphiphiles with an amino acid residue exhibit a potent anti-protozoan activity and are cytotoxic towards a wide array of protozoal parasites, which includes Indian varieties of Leishmania donovani and also kill resistant parasitic strains including BHU-575, MIL^R and CPT^R cells. These gelators are highly cytotoxic to promastigotes of Leishmania and trigger apoptotic-like events inside the parasite. The mechanism of killing the parasite is shown and these gelators are non-cytotoxic to host macrophage cells indicating the potential use of these gels as therapeutic agents against multiple forms of leishmaniasis in the near future.

Short Peptide-based Cross-β Amyloids Exploit Dual Residues for Phosphoesterase like Activity

Herein, we report that short peptides are capable of exploiting their anti-parallel registry to access cross-β stacks to expose more than one catalytic residue, exhibiting the traits of advanced binding pockets of enzymes. Binding pockets decorated with more than one catalytic residue facilitate substrate binding and process kinetically unfavourable chemical transformations. The solvent-exposed guanidinium and imidazole moieties on the cross-β microphases synergistically bind to polarise and hydrolyse diverse kinetically stable model substrates of nucleases and phosphatase. Mutation of either histidine or arginine results in a drastic decline in the rate of hydrolysis. These results not only support the argument of short amyloid peptides as the earliest protein folds but also suggest their interactions with nucleic acid congeners, foreshadowing the mutualistic biopolymer relationships that fueled the chemical emergence of life.

Amyloid based short peptide assemblies use antiparallel registry to expose multiple catalytic residues to bind and cleave kinetically stable phosphoester bonds of nucleic acid congeners, foreshadowing interactions of protein folds with nucleic acids.