Computational design of peptide therapeutics: how useful are sequence-based protein-protein interaction predictors?

Engineering peptides to achieve a desired therapeutic effect through the inhibition of a specific target activity or protein interaction is a non-trivial task. Few of the existing in silico peptide design algorithms generate target-specific peptides. Instead, many methods produce peptides that achieve a desired effect through an unknown mechanism. In contrast with resource-intensive high-throughput experiments, in silico screening is a cost-effective alternative that can prune the space of candidates when engineering target-specific peptides. Using a set of FDA-approved peptides we curated specifically for this task, we assess the applicability of several sequence-based protein-protein interaction predictors as a screening tool within the context of peptide therapeutic engineering. We show that similarity-based protein-protein interaction predictors are more suitable for this purpose than the current state-of-the-art deep learning methods. We also show that this approach is mostly useful when designing new peptides against targets for which naturally-occurring interactors are already known, and that deploying it for de novo peptide engineering tasks may require gathering additional target-specific training data. Taken together, this work offers evidence that supports the use of similarity-based protein-protein interaction predictors for peptide therapeutic engineering, especially peptide analogs.

Improved Production of Xylanase in Pichia pastoris and Its Application in Xylose Production From Xylan

Xylanases with high specific activity has been focused with great interest as a useful enzyme in biomass utilization. The production of recombinant GH11 xylanase (MYCTH_56237) from Myceliophthora thermophila has been improved through N-terminal signal peptide engineering in P. pastoris. The production of newly recombinant xylanase (termed Mtxyn11C) was improved from 442.53 to 490.7 U/mL, through a replacement of α-factor signal peptide with the native xylanase signal peptide segment (MVSVKAVLLLGAAGTTLA) in P. pastoris. Scaling up of Mtxyn11C production in a 7.5 L fermentor was improved to the maximal production rate of 2503 U/mL. In this study, the degradation efficiency of Mtxyn11C was further examined. Analysis of the hydrolytic mode of action towards the birchwood xylan (BWX) revealed that Mtxyn11C was clearly more effective than commercial xylanase and degrades xylan into xylooligosaccharides (xylobiose, xylotriose, xylotetraose). More importantly, Mtxyn11C in combination with a single multifunctional xylanolytic enzyme, improved the hydrolysis of BWX into single xylose by 40%. Altogether, this study provided strategies for improved production of xylanase together with rapid conversion of xylose from BWX, which provides sustainable, cost-effective and environmental friendly approaches to produce xylose/XOSs for biomass energy or biofuels production.

Special Issue: Advances of Peptide Engineering

Peptides have been gaining increasing attention for their applications in various fields, such as medical, biotechnological, and nanotechnological fields [...]

Extracting and Interpreting the Effects of Higher Order Sequence Features on Peptide MHC Binding

Understanding the factors contributing to peptide MHC (pMHC) affinity is critical for the study of immune responses and the development of novel therapeutics. Developments in yeast display platforms have enabled the collection of pMHC binding data for vast libraries of peptides. However, methods for interpreting this data are still at an early stage. In this work we propose an approach for extracting peptide sequence features that affect pMHC binding from such datasets. In the process we develop the theoretical framework for fitting and interpreting these features. We demonstrate that these features accurately capture the kinetics underlying pMHC binding, and can be used to predict pMHC binding well enough to rival the current state of the art. We then analyze the extracted factors and show that they correlate with our current structural understanding of MHC molecules. Finally, we discuss the implication these factors have on the complexity of peptide engineering.

Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells

<a></a><a>Peptide engineering has been extremely successful in creating new structures with defined properties and functions. Although generally overlooked in this context, coordination chemistry offers an additional set of interactions that opens unexplored design opportunities for developing complex molecular structures. With this in mind, we report the development of new artificial peptide ligands that fold into chiral and discrete supramolecular helicates in the presence of labile metal ions such as Fe(II) and Co(II). By selecting appropriate heterochiral β‑turn promoting sequences, we can encode the stereoselective folding of the peptide ligand, and define the physicochemical properties of their corresponding metal complexes. The study of these metallopeptides by CD and NMR spectroscopy, combined with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. </a>We also show that these new peptide helicates, dynamically selected in the presence of labile Co(II) ions, can be locked as kinetically-inert species by <i>in situ</i> oxidation to Co(III). Finally, in addition to the <i>in vitro</i> characterization of their selective binding to three-way DNA, cell microscopy experiments demonstrated that a rhodamine-labeled Fe(II) helicate was internalized and selectively stains DNA replication factories in functional cells.

Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells

<a></a><a>Peptide engineering has been extremely successful in creating new structures with defined properties and functions. Although generally overlooked in this context, coordination chemistry offers an additional set of interactions that opens unexplored design opportunities for developing complex molecular structures. With this in mind, we report the development of new artificial peptide ligands that fold into chiral and discrete supramolecular helicates in the presence of labile metal ions such as Fe(II) and Co(II). By selecting appropriate heterochiral β‑turn promoting sequences, we can encode the stereoselective folding of the peptide ligand, and define the physicochemical properties of their corresponding metal complexes. The study of these metallopeptides by CD and NMR spectroscopy, combined with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. </a>We also show that these new peptide helicates, dynamically selected in the presence of labile Co(II) ions, can be locked as kinetically-inert species by <i>in situ</i> oxidation to Co(III). Finally, in addition to the <i>in vitro</i> characterization of their selective binding to three-way DNA, cell microscopy experiments demonstrated that a rhodamine-labeled Fe(II) helicate was internalized and selectively stains DNA replication factories in functional cells.

Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells

<a></a><a>Peptide engineering has been extremely successful in creating new structures with defined properties and functions. Although generally overlooked in this context, coordination chemistry offers an additional set of interactions that opens unexplored design opportunities for developing complex molecular structures. With this in mind, we report the development of new artificial peptide ligands that fold into chiral and discrete supramolecular helicates in the presence of labile metal ions such as Fe(II) and Co(II). By selecting appropriate heterochiral β‑turn promoting sequences, we can encode the stereoselective folding of the peptide ligand, and define the physicochemical properties of their corresponding metal complexes. The study of these metallopeptides by CD and NMR spectroscopy, combined with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. </a>We also show that these new peptide helicates, dynamically selected in the presence of labile Co(II) ions, can be locked as kinetically-inert species by <i>in situ</i> oxidation to Co(III). Finally, in addition to the <i>in vitro</i> characterization of their selective binding to three-way DNA, cell microscopy experiments demonstrated that a rhodamine-labeled Fe(II) helicate was internalized and selectively stains DNA replication factories in functional cells.