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

Advances in therapeutic peptides targeting G protein-coupled receptors.

Dysregulation of peptide-activated pathways causes a range of diseases, fostering the discovery and clinical development of peptide drugs. Many endogenous peptides activate G protein-coupled receptors (GPCRs) - nearly 50 GPCR peptide drugs have been approved to date, most of them for metabolic disease or oncology, and more than 10 potentially first-in-class peptide therapeutics are in the pipeline. The majority of existing peptide therapeutics are agonists, which reflects the currently dominant strategy of modifying the endogenous peptide sequence of ligands for peptide-binding GPCRs. Increasingly, novel strategies are being employed to develop both agonists and antagonists, to both introduce chemical novelty and improve drug-like properties. Pharmacodynamic improvements are evolving to allow biasing ligands to activate specific downstream signalling pathways, in order to optimize efficacy and reduce side effects. In pharmacokinetics, modifications that increase plasma half-life have been revolutionary. Here, we discuss the current status of the peptide drugs targeting GPCRs, with a focus on evolving strategies to improve pharmacokinetic and pharmacodynamic properties.Wellcome Trust [WT107715/Z/15/Z], Cambridge Biomedical Research Centre Biomedical Resources Gran

In vivo therapeutic efficacy of frog skin-derived peptides against Pseudomonas aeruginosa-induced pulmonary infection

Pseudomonas aeruginosa is an opportunistic and frequently drug-resistant pulmonary pathogen especially in cystic fibrosis sufferers. Recently, the frog skin-derived antimicrobial peptide (AMP) Esc(1-21) and its diastereomer Esc(1-21)-1c were found to possess potent in vitro antipseudomonal activity. Here, they were first shown to preserve the barrier integrity of airway epithelial cells better than the human AMP LL-37. Furthermore, Esc(1-21)-1c was more efficacious than Esc(1-21) and LL-37 in protecting host from pulmonary bacterial infection after a single intra-tracheal instillation at a very low dosage of 0.1 mg/kg. The protection was evidenced by 2-log reduction of lung bacterial burden and was accompanied by less leukocytes recruitment and attenuated inflammatory response. In addition, the diastereomer was more efficient in reducing the systemic dissemination of bacterial cells. Importantly, in contrast to what reported for other AMPs, the peptide was administered at 2 hours after bacterial challenge to better reflect the real life infectious conditions. To the best of our knowledge, this is also the first study investigating the effect of AMPs on airway-epithelia associated genes upon administration to infected lungs. Overall, our data highly support advanced preclinical studies for the development of Esc(1-21)-1c as an efficacious therapeutic alternative against pulmonary P. aeruginosa infection

Development of analgesic peptide therapeutics for AIDS-related neuropathic pain

poster abstractChronic neuropathic pain is a huge problem to the health and well-being of an increasingly ageing population in the US, as substantiated by the large unmet clinical need associated with this type of pain, with estimates of 30-50% of sufferers refractory to existing medication. Thus, there is an imperative to increase knowledge of mechanisms of action of the key proteins in nociceptive pathways in vitro and to extend this knowledge to in vivo models of neuropathy to advance therapeutic development in this area. N-type voltage-gated Ca2+ channels (CaV2.2) have emerged as potential novel targets for the treatment of chronic neuropathic pain. Funded, in part, by a FORCES grant, we have identified two novel derivatives of the parent 15 amino acid CBD3 peptide, derived from collapsin response mediator protein 2 (CRMP-2) that suppressed inflammatory and neuropathic hypersensitivity by inhibiting CRMP-2 binding to N-type voltage gated calcium channels (CaV2.2) [Brittain et al., Nature Medicine 17:822-829 (2011)]. Pharmacokinetic studies revealed nanogram levels of peptide in plasma of rats systemic administration consistent with relief of hypersensitivity. Furthermore, we observed improved and broader efficacy of the derivatized peptides in AIDS-therapy and nerve-injury related neuropathic pain models. Future studies regarding dosing and route of delivery optimization as well as identification of peptide-mimetics are ongoing to fully realize the commercial value of the peptides. Supported by the Startup program at the Indiana University Research & Technology Corporation (IURTC), we have setup Sophia Therapeutics LLC and together with IURTC are committed to the work proposed here

Molecular Peptide Grafting as a Tool to Create Novel Protein Therapeutics

The study of peptides (synthetic or corresponding to discrete regions of proteins) has facilitated the understanding of protein structure-activity relationships. Short peptides can also be used as powerful therapeutic agents. However, the functional activity of many short peptides is usually substantially lower than that of their parental proteins. This is (as a rule) due to their diminished structural organization, stability, and solubility often leading to an enhanced propensity for aggregation. Several approaches have emerged to overcome these limitations, which are aimed at imposing structural constraints into the backbone and/or sidechains of the therapeutic peptides (such as molecular stapling, peptide backbone circularization and molecular grafting), therefore enforcing their biologically active conformation and thus improving their solubility, stability, and functional activity. This review provides a short summary of approaches aimed at enhancing the biological activity of short functional peptides with a particular focus on the peptide grafting approach, whereby a functional peptide is inserted into a scaffold molecule. Intra-backbone insertions of short therapeutic peptides into scaffold proteins have been shown to enhance their activity and render them a more stable and biologically active conformation

An Alternate View of Neuroprotection with Peptides in Alzheimer’s Disease

Neuroprotection plays a crucial role in everyday life, maintaining a clean environment in the central nervous system to allow for normal functioning. In Alzheimer’s disease and other neurodegenerative disorders, neuroprotection may have two roles. Under standard circumstances, the immune system protects the CNS, but sometimes it can exacerbate the pathophysiology of some diseases through neuroinflammation leading to further degeneration. Alzheimer’s disease is fast getting out of control, with no new approvals in therapeutics since 2003, and of those approved, all target symptomatic treatment. Initiated by a microglial response to Aβ plaques, therapeutic development should focus on the amyloid cascade as a neuroprotective measure for Alzheimer’s disease. This chapter will examine the status of the types of therapeutics in clinical trials for Alzheimer’s disease, offering insights into peptides as an area of opportunity for neuroprotection and detailing considerations for the use of peptides in Alzheimer’s disease

Developing a Dissociative Nanocontainer for Peptide Drug Delivery

The potency, selectivity, and decreased side effects of bioactive peptides have propelled these agents to the forefront of pharmacological research. Peptides are especially promising for the treatment of neurological disorders and pain. However, delivery of peptide therapeutics often requires invasive techniques, which is a major obstacle to their widespread application. We have developed a tailored peptide drug delivery system in which the viral capsid of P22 bacteriophage is modified to serve as a tunable nanocontainer for the packaging and controlled release of bioactive peptides. Recent efforts have demonstrated that P22 nanocontainers can effectively encapsulate analgesic peptides and translocate them across blood-brain-barrier (BBB) models. However, release of encapsulated peptides at their target site remains a challenge. Here a Ring Opening Metathesis Polymerization (ROMP) reaction is applied to trigger P22 nanocontainer disassembly under physiological conditions. Specifically, the ROMP substrate norbornene (5-Norbornene-2-carboxylic acid) is conjugated to the exterior of a loaded P22 nanocontainer and Grubbs II Catalyst is used to trigger the polymerization reaction leading to nanocontainer disassembly. Our results demonstrate initial attempts to characterize the ROMP-triggered release of cargo peptides from P22 nanocontainers. This work provides proof-of-concept for the construction of a triggerable peptide drug delivery system using viral nanocontainers