Gastroresistant oral peptide for fluorescence imaging of colonic inflammation

Gastrointestinal Permeation Enhancers Beyond Sodium Caprate and SNAC - What is Coming Next?

Oral peptide delivery is trending again. Among the possible reasons are the recent approvals of two oral peptide formulations, which represent a huge stride in the field. For the first time, gastrointestinal (GI) permeation enhancers (PEs) are leveraged to overcome the main limitation of oral peptide delivery-low permeability through the intestinal epithelium. Despite some success, the application of current PEs, such as salcaprozate sodium (SNAC), sodium caprylate (C8), and sodium caprate (C10), is generally resulting in relatively low oral bioavailabilities (BAs)-even for carefully selected therapeutics. With several hundred peptide-based drugs presently in the pipeline, there is a huge unmet need for more effective PEs. Aiming to provide useful insights for the development of novel PEs, this review summarizes the biological hurdles to oral peptide delivery with special emphasis on the epithelial barrier. It describes the concepts and action modes of PEs and mentions possible new targets. It further states the benchmark that is set by current PEs, while critically assessing and evaluating emerging PEs regarding translatability, safety, and efficacy. Additionally, examples of novel PEs under preclinical and clinical evaluation and future directions are discussed.

Advancing oral delivery of biologics: Machine learning predicts peptide stability in the gastrointestinal tract

The oral delivery of peptide therapeutics could facilitate precision treatment of numerous gastrointestinal (GI) and systemic diseases with simple administration for patients. However, the vast majority of licensed peptide drugs are currently administered parenterally due to prohibitive peptide instability in the GI tract. As such, the development of GI-stable peptides is receiving considerable investment. This study provides researchers with the first tool to predict the GI stability of peptide therapeutics based solely on the amino acid sequence. Both unsupervised and supervised machine learning techniques were trained on literature-extracted data describing peptide stability in simulated gastric and small intestinal fluid (SGF and SIF). Based on 109 peptide incubations, classification models for SGF and SIF were developed. The best models utilized k-Nearest Neighbor (for SGF) and XGBoost (for SIF) algorithms, with accuracies of 75.1% (SGF) and 69.3% (SIF), and f1 scores of 84.5% (SGF) and 73.4% (SIF) under 5-fold cross-validation. Feature importance analysis demonstrated that peptides' lipophilicity, rigidity, and size were key determinants of stability. These models are now available to those working on the development of oral peptide therapeutics.

Metadynamics to Enhance Sampling in Biomolecular Simulations

Molecular dynamics is a powerful simulation method to provide detailed atomic-scale insight into a range of biological processes including protein folding, biochemical reactions, ligand binding, and many others. Over the last several decades, enhanced sampling methods have been developed to address the large separation in time scales between a molecular dynamics simulation (usually microseconds or shorter) and the time scales of biological processes (often orders of magnitude longer). This chapter specifically focuses on the metadynamics family of methods, which achieves enhanced sampling through the introduction of a history-dependent bias potential that is based on one or more slow degrees of freedom, called collective variables. We introduce the method and its recent variants related to biomolecular studies and then discuss frontier areas of the method. A large part of this chapter is devoted to helping new users of the method understand how to choose metadynamics parameters properly and apply the method to their system of interest.

Peptide and protein mimetics by retro and retroinverso analogs

Retroinverso analog of a natural polypeptide can sometimes mimic the structure and function of the natural peptide. The additional advantage of using retroinverso analog is that it is resistant to proteolysis. The retroinverso analogs have peptide sequence in reverse direction with respect to natural peptide and also have chirality of amino acid inverted from L to D. The D amino acids cannot be recognized by common proteases of the body; therefore, these peptides will not be degraded easily and have a longer-lasting effect as vaccine and inhibitor drugs. There have been many contested propositions about the geometric relationship between a peptide and its retro, inverso, or retroinverso analog. A retroinverso analog sometimes fails to adopt the structure that can mimic the function of the natural peptide. In such cases, partial retroinverso analog and other modifications can help in achieving the desired structure and function. Here, we review the theory, major experimental attempts, prediction methods, and alternative strategies related to retroinverso peptidomimetics.