SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders.

Protein-protein interactions (PPIs) are critical for biological processes and predicting the sites of these interactions is useful for both computational and experimental applications. We present a Structure-agnostic Language Transformer and Peptide Prioritization (SaLT&PepPr) pipeline to predict interaction interfaces from a protein sequence alone for the subsequent generation of peptidic binding motifs. Our model fine-tunes the ESM-2 protein language model (pLM) with a per-position prediction task to identify PPI sites using data from the PDB, and prioritizes motifs which are most likely to be involved within inter-chain binding. By only using amino acid sequence as input, our model is competitive with structural homology-based methods, but exhibits reduced performance compared with deep learning models that input both structural and sequence features. Inspired by our previous results using co-crystals to engineer target-binding "guide" peptides, we curate PPI databases to identify partners for subsequent peptide derivation. Fusing guide peptides to an E3 ubiquitin ligase domain, we demonstrate degradation of endogenous ß-catenin, 4E-BP2, and TRIM8, and highlight the nanomolar binding affinity, low off-targeting propensity, and function-altering capability of our best-performing degraders in cancer cells. In total, our study suggests that prioritizing binders from natural interactions via pLMs can enable programmable protein targeting and modulation.

Isolation of full-length IgG antibodies from combinatorial libraries expressed in the cytoplasm of Escherichia coli.

Here we describe a facile and robust genetic selection for isolating full-length IgG antibodies from combinatorial libraries expressed in the cytoplasm of redox-engineered Escherichia coli cells. The method is based on the transport of a bifunctional substrate comprised of an antigen fused to chloramphenicol acetyltransferase, which allows positive selection of bacterial cells co-expressing cytoplasmic IgGs called cyclonals that specifically capture the chimeric antigen and sequester the antibiotic resistance marker in the cytoplasm. The utility of this approach is first demonstrated by isolating affinity-matured cyclonal variants that specifically bind their cognate antigen, the leucine zipper domain of a yeast transcriptional activator, with subnanomolar affinities, which represent a ~20-fold improvement over the parental IgG. We then use the genetic assay to discover antigen-specific cyclonals from a naïve human antibody repertoire, leading to the identification of lead IgG candidates with affinity and specificity for an influenza hemagglutinin-derived peptide antigen.

Profiling Germinal Center-like B Cell Responses to Conjugate Vaccines Using Synthetic Immune Organoids.

Glycoengineered bacteria have emerged as a cost-effective platform for rapid and controllable biosynthesis of designer conjugate vaccines. However, little is known about the engagement of such conjugates with naïve B cells to induce the formation of germinal centers (GC), a subanatomical microenvironment that converts naïve B cells into antibody-secreting plasma cells. Using a three-dimensional biomaterials-based B-cell follicular organoid system, we demonstrate that conjugates triggered robust expression of hallmark GC markers, B cell receptor clustering, intracellular signaling, and somatic hypermutation. These responses depended on the relative immunogenicity of the conjugate and correlated with the humoral response in vivo. The occurrence of these mechanisms was exploited for the discovery of high-affinity antibodies against components of the conjugate on a time scale that was significantly shorter than for typical animal immunization-based workflows. Collectively, these findings highlight the potential of synthetic organoids for rapidly predicting conjugate vaccine efficacy as well as expediting antigen-specific antibody discovery.

Congo Red Decolorization Using Textile Filters and Laccase-Based Nanocomposites in Continuous Flow Bioreactors.

Removal of azo and diazo dye content from textile industry wastewaters is crucial due to their environmental impact. Here, we report on the use of the fungal laccase from Pycnoporus sanguineus CS43 immobilized on silica nanoparticles and entrapped in textile-based filters for the degradation of Congo Red. Laccase immobilization and synthesis of the nanocomposites were carried out by two different methods, one in the presence of acetone and the second using water as solvent. This led to a change in the hydrophobicity of the obtained biofilters. Successful preparation of the nanocomposites was confirmed via FTIR spectroscopy. Changes in the secondary structure of the enzyme were inspected through the second derivative of the FTIR spectra. Six different types of filter were fabricated and tested in a continuous flow bioreactor in terms of their decolorization capabilities of Congo Red. The results indicate removal efficiencies that approached 40% for enzymes immobilized on the more hydrophobic supports. Backscattered electron (BSE) images of the different filters were obtained before and after the decolorization process. Percentage of decolorization and activity loss were determined as a function of time until a plateau in decolorization activity was reached. Experimental data was used to recreate the decolorization process in COMSOL Multiphysics® (Stockholm, Sweden). These simulations were used to determine the proper combination of parameters to maximize decolorization. Our findings suggest that the treatment of textile-based filters with immobilized laccase in conjunction with hydrophobic nanocomposites provides a suitable avenue to achieve more efficient laccase dye decolorization (39%) than that obtained with similar filters treated only with free laccase (8%). Filters treated with silica-based nanocomposites and immobilized laccases showed an increase in their decolorization capability, probably due to changes in their wetting phenomena.

Enhanced Catalytic Dye Decolorization by Microencapsulation of Laccase from P. Sanguineus CS43 in Natural and Synthetic Polymers.

Polymeric microcapsules with the fungal laccase from Pycnoporus sanguineus CS43 may represent an attractive avenue for the removal or degradation of dyes from wastewaters. Microcapsules of alginate/chitosan (9.23 ± 0.12 µm) and poly(styrenesulfonate) (PSS) (9.25 ± 0.35 µm) were synthesized and subsequently tested for catalytic activity in the decolorization of the diazo dye Congo Red. Successful encapsulation into the materials was verified via confocal microscopy of labeled enzyme molecules. Laccase activity was measured as a function of time and the initial reaction rates were recovered for each preparation, showing up to sevenfold increase with respect to free laccase. The ability of substrates to diffuse through the pores of the microcapsules was evaluated with the aid of fluorescent dyes and confocal microscopy. pH and thermal stability were also measured for encapsulates, showing catalytic activity for pH values as low as 4 and temperatures of about 80 °C. Scanning electron microscope (SEM) analyses demonstrated the ability of PSS capsules to avoid accumulation of byproducts and, therefore, superior catalytic performance. This was corroborated by the direct observation of substrates diffusing in and out of the materials. Compared with our PSS preparation, alginate/chitosan microcapsules studied by others degrade 2.6 times more dye, albeit with a 135-fold increase in units of enzyme per mg of dye. Similarly, poly(vinyl) alcohol microcapsules from degrade 1.7 times more dye, despite an eightfold increase in units of enzyme per mg of dye. This could be potentially beneficial from the economic viewpoint as a significantly lower amount of enzyme might be needed for the same decolorization level achieved with similar encapsulated systems.

Multifunctional magnetite nanoparticles to enable delivery of siRNA for the potential treatment of Alzheimer's.

Therapeutic drugs for Alzheimer's disease have been extensively studied due to its recurrence and abundance among neurodegenerative diseases. It is thought that the accumulation of amyloid precursor protein (APP) products, a consequence of an up-regulation of the ß-site APP-cleaving enzyme 1 (BACE1), is the main triggering mechanism during the early stages of the disease. This study aims to explore the ability of a multifunctional conjugate based on magnetite nanoparticles for the cellular delivery of siRNA against the expression of the BACE1 gene. We immobilized the siRNA strand on PEGylated magnetite nanoparticles and investigated the effects on biocompatibility and efficacy of the conjugation. Similarly, we co-immobilized the translocating protein OmpA on PEGylated nanoparticles to enhance cellular uptake and endosomal escape. BACE1 suppression was statistically significant in HFF-1 cells, without any presence of a cytotoxic effect. The delivery of the nanoconjugate was achieved through endocytosis pathways, where endosome formation was likely escaped due to the proton-sponge effect characteristic of PEGylated nanoparticles or mainly by direct translocation in the case of OmpA/PEGylated nanoparticles.

Magnetite-OmpA Nanobioconjugates as Cell-Penetrating Vehicles with Endosomal Escape Abilities.

Outer membrane protein A (OmpA) has been extensively studied in Gram-negative bacteria due to its relevance in the adhesion of pathogens to host cells and its surfactant capabilities. It consists of a hydrophobic ß-barrel domain and a hydrophilic periplasmic domain, that confers OmpA an amphiphilic structure. This study aims to elucidate the capacity of Escherichia coli OmpA to translocate liposomal membranes and serve as a potential cell-penetrating vehicle. We immobilized OmpA on magnetite nanoparticles and investigated the possible functional changes exhibited by OmpA after immobilization. Liposomal intake was addressed using egg lecithin liposomes as a model, where magnetite-OmpA nanobioconjugates were able to translocate the liposomal membrane and caused a disruptive effect when subjected to a magnetic field. Nanobioconjugates showed both low cytotoxicity and hemolytic tendency. Additional interactions within the intracellular space led to altered viability results via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). Confocal microscopy images revealed that immobilized nanoparticles effectively enter the cytoplasm of THP-1 and Vero cells by different routes, and, subsequently, some escape endosomes, lysosomes, and other intracellular compartments with relatively high efficiencies. This was demonstrated by co-localization analyses with LysoTracker green that showed Pearson correlations of about 80 and 28%.

The future point-of-care detection of disease and its data capture and handling.

Point-of-care detection is a widely studied area that attracts effort and interest from a large number of fields and companies. However, there is also increased interest from the general public in this type of device, which has driven enormous changes in the design and conception of these developments and the way data is handled. Therefore, future point-of-care detection has to include communication with front-end technology, such as smartphones and networks, automation of manufacture, and the incorporation of concepts like the Internet of Things (IoT) and cloud computing. Three key examples, based on different sensing technology, are analyzed in detail on the basis of these items to highlight a route for the future design and development of point-of-care detection devices and their data capture and handling.