Combining mass spectrometry and machine learning to discover bioactive peptides

Peptides play important roles in regulating biological processes and form the basis of a multiplicity of therapeutic drugs. To date, only about 300 peptides in human have confirmed bioactivity, although tens of thousands have been reported in the literature. The majority of these are inactive degradation products of endogenous proteins and peptides, presenting a needle-in-a-haystack problem of identifying the most promising candidate peptides from large-scale peptidomics experiments to test for bioactivity. To address this challenge, we conducted a comprehensive analysis of the mammalian peptidome across seven tissues in four different mouse strains and used the data to train a machine learning model that predicts hundreds of peptide candidates based on patterns in the mass spectrometry data. We provide in silico validation examples and experimental confirmation of bioactivity for two peptides, demonstrating the utility of this resource for discovering lead peptides for further characterization and therapeutic development.

Sintering of Inkjet-printed Cu-nanoparticle Ink in Ambient Conditions Using a Continuous Wave 808 nm Diode Laser

In this paper, we focused on sintering of inkjet-printed copper nanoparticle ink structures using a continuous wave 808nm diode laser. Laser sintering in printed electronics is a rapid sintering method which enables localized sintering. Sintering of Cu inks is usually done in nitrogen atmosphere but the novelty of this study is that successful sintering of Cu ink was done under ambient conditions. The used ink consists of copper nanoparticles covered with a dispersion agent. Photonic sintering is needed to speed up the sintering process to prevent oxidation during sintering. Electrical and mechanical performance of the printed structures was analyzed. Resistivity of 10-12 μΩcm with good repeatability as well as excellent adhesion, were achieved.

To conjugate or not to conjugate? evaluating the potential use of cell-penetrating peptides for conjugation or complexation with oligonucleotides by surface plasmon resonance

Oligonucleotides represent a class of molecules that exhibit remarkable therapeutic potential due to their unparalleled target specificity, yet they suffer from limited cellular uptake and lack of tissue selectivity. Extensive research is conducted with cell-penetrating peptides (CPPs) as delivery excipients due to their ability to translocate across cellular membranes and deliver cargo into cells. This study aims to investigate an innovative approach to rapidly, and with small amounts of compound, analyze and compare complexation of CPPs to oligonucleotides. The study applies surface plasmon resonance (SPR) to evaluate a comprehensive library of CPPs regarding their interaction with a double-stranded oligonucleotide to assess their potential as complexing molecules or whether the CPP should be chemically linked to the negatively charged oligonucleotide to ensure proximity. Specifically, a small interfering RNA (siRNA) was immobilized on a biotinylated chip, and solutions of 66 CPPs were subsequently injected to determine their binding stoichiometry with the siRNA. The most influential molecular properties of the CPPs were determined to be the positive charge-to-length ratio, the total number of positive charges, and the overall hydrophobicity of the CPP. These findings demonstrate the effectiveness and utility of SPR as a high throughput screening tool for selecting peptide/oligonucleotide pairs intended for complexation or conjugation.

Impact of Stress on the Immunogenic Potential of Adalimumab

Monoclonal antibodies against tumor necrosis factor-alpha (TNFα) are widely used for treatment of inflammatory diseases. However, despite the inhibitory effect this class of drugs has on the immune system, anti-drug antibodies are often formed with continuous use. Particles formed during stress conditions, which can be used to simulate storage and handling conditions of commercial antibodies, have previously been associated with the formation of anti-drug antibodies. This study investigates the relationship between particles, oligomerization, folding and chemical degradation on the in vitro cytokine response toward the TNFα inhibitor adalimumab. Adalimumab aggregates generated using stir and heat stress were fractionated into distinct sub-populations, and their structure and immunogenic potential were evaluated. A chemically degraded sample of adalimumab was included to compare particle composition with the milder accelerated heat and stir stressed conditions. Particles from stressed adalimumab samples induced elevated cytokine levels and CD4+ T cell proliferation in vitro compared to non-stressed samples. Samples enriched with both submicron and subvisible particles of adalimumab induced the strongest cytokine release and the strongest CD4+ T cell proliferation despite maintaining some TNFα inhibitory functionality. Samples that were stressed and subsequently purified of subvisible and submicron particles did not elicit a significantly higher cytokine response or show increased CD4+ T cell proliferation compared to a non-stressed sample. Oxidation-induced chemical modifications in adalimumab, mainly in Met, His, Trp, and Tyr, were not found to be sufficient in absence of particle formation to induce increased CD4+ T cell proliferation or cytokine release despite less decreased TNFα inhibitory activity of adalimumab. These observations provide further evidence that particles do indeed potentiate the immunogenic potential of adalimumab.