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Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid.

ABSTRACT: Protein-based targeting reagents, such as antibodies and non-antibody scaffold proteins, are rapidly inactivated in the upper gastrointestinal (GI) tract. Hydrochloric acid in gastric juice denatures proteins and activates pepsin, concentrations of which reach 1 mg/mL in the mammalian stomach. Two stable scaffold proteins (nanobody and nanofitin), previously developed to be protease-resistant, were completely digested in less than 10 min at 100-fold lower concentration of pepsin than found in the stomach. Here we present gastrobodies, a protein scaffold derived from Kunitz soybean trypsin inhibitor (SBTI). SBTI is highly resistant to the challenges of the upper GI tract, including digestive proteases, pH 2 and bile acids. Computational prediction of SBTI's evolvability identified two nearby loops for randomization, to create a potential recognition surface which was experimentally validated by alanine scanning. We established display of SBTI on full-length pIII of M13 phage. Phage selection of gastrobody libraries against the glucosyltransferase domain of Clostridium difficile toxin B (GTD) identified hits with nanomolar affinity and enzyme inhibitory activity. Anti-GTD binders retained high stability to acid, digestive proteases and heat. Gastrobodies show resilience to exceptionally harsh conditions, which should provide a foundation for targeting and modulating function within the GI tract.

SUBMITTER: Wicke N

PROVIDER: S-EPMC8358037 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Gastrobodies are engineered antibody mimetics resilient to pepsin and hydrochloric acid

Project description:Protein-based targeting reagents, such as antibodies and non-antibody scaffold proteins, are rapidly inactivated in the upper gastrointestinal (GI) tract. Hydrochloric acid in gastric juice denatures proteins and activates pepsin, concentrations of which reach 1 mg/mL in the mammalian stomach. Here we present gastrobodies, a protein scaffold derived from Kunitz soybean trypsin inhibitor (SBTI). SBTI is highly resistant to the challenges of the upper GI tract, including digestive proteases, pH 2 and bile acids. Computational prediction of SBTI’s evolvability identified two nearby loops for randomization, to create a potential recognition surface which was experimentally validated by alanine scanning. We established display of SBTI on full-length pIII of M13 phage. Phage selection of gastrobody libraries against the glucosyltransferase domain of Clostridium difficile toxin B (GTD) identified hits with nanomolar affinity and enzyme inhibitory activity. Anti-GTD binders retained high stability to acid, digestive proteases and heat. We use mass spectrometry to identify cut sites outside of the gastrobody.

2021-08-13 | PXD027071 | Pride

Fc-Small Molecule Antibody Mimetics.

Project description:Antibody therapeutics are a promising drug class due to their high specificity and favorable pharmacokinetics. While there are many methods for the development of antibodies specific to disease associated antigens, selecting antibodies against functional epitopes with high specificity and affinity can be difficult for certain epitopes. We describe a generalizable method for synthesizing antibody mimetics by site specifically conjugating small molecules (with high affinity and specificity to disease associated antigens) to an Fc fragment to develop drugs with the benefits of an antibody. As a proof of concept, an E269pAcPhe Fc antibody Fc fragment was produced and subsequently site-specifically labeled with a linker-modified folic acid compound to generate an Fc-folic acid antibody-mimetic. This was chosen as the model system because the high-affinity folate receptor FR-α is highly expressed in a number of cancer types including breast and ovarian cancer. The specificity of the Fc-folic acid conjugate was assessed via flowcytometry with the folate-receptor positive breast cancer cell line MDA-MB-231 by measuring Fc-folic acid binding in both the absence and presence of an excess of folic acid. Fc-small molecule conjugates could be developed into a unique class of antibody-like therapeutics.

| S-EPMC6667356 | biostudies-literature

Pepsin Triggers Neutrophil Migration Across Acid Damaged Lung Epithelium.

Project description:Pepsin represents a potential biomarker for extraesophageal reflux disease when detected in airways, however a direct role for pepsin in lung dysfunction has not been clearly established. Children experiencing gastroesophageal and extraesophageal reflux are often prescribed proton pump inhibitors (PPIs) to reduce gastric acid associated damage to esophageal and airway mucosa. The potential of pepsin and gastric fluid, from children that were either on or off PPI therapy, to cause inflammation and damage using a human in vitro co-culture model of the airway mucosa was evaluated herein. Exposure of the airway model to acidic solutions caused cellular damage and loss of viability, however, acid alone did not disrupt barrier integrity or instigate neutrophil trans-epithelial migration without pepsin. Gastric fluid from patients on PPI therapy exhibited only a slightly higher pH yet had significantly higher concentrations of pepsin and elicited more barrier disruption and neutrophil trans-epithelial migration compared to gastric fluid from patients off PPIs. Inflammatory and damaging responses observed with gastric fluid from patients on PPIs were largely driven by pepsin. These results indicate the potential for PPI usage to raise concentrations of pepsin in gastric fluid, which may enhance the pathological impact of micro-aspirations in children with extraesophageal reflux.

| S-EPMC6760148 | biostudies-literature

Direct anodic hydrochloric acid and cathodic caustic production during water electrolysis.

Project description:Hydrochloric acid (HCl) and caustic (NaOH) are among the most widely used chemicals by the water industry. Direct anodic electrochemical HCl production by water electrolysis has not been successful as current commercially available electrodes are prone to chlorine formation. This study presents an innovative technology simultaneously generating HCl and NaOH from NaCl using a Mn0.84Mo0.16O2.23 oxygen evolution electrode during water electrolysis. The results showed that protons could be anodically generated at a high Coulombic efficiency (i.e. ≥ 95%) with chlorine formation accounting for 3 ~ 5% of the charge supplied. HCl was anodically produced at moderate strengths at a CE of 65 ± 4% together with a CE of 89 ± 1% for cathodic caustic production. The reduction in CE for HCl generation was caused by proton cross-over from the anode to the middle compartment. Overall, this study showed the potential of simultaneous HCl and NaOH generation from NaCl and represents a major step forward for the water industry towards on-site production of HCl and NaOH. In this study, artificial brine was used as a source of sodium and chloride ions. In theory, artificial brine could be replaced by saline waste streams such as Reverse Osmosis Concentrate (ROC), turning ROC into a valuable resource.

| S-EPMC4742805 | biostudies-literature

Design of Smart Antibody Mimetics with Photosensitive Switches.

Project description:As two prominent examples of intracellular single-domain antibodies or antibody mimetics derived from synthetic protein scaffolds, monobodies and nanobodies are gaining wide applications in cell biology, structural biology, synthetic immunology, and theranostics. Herein, a generally applicable method to engineer light-controllable monobodies and nanobodies, designated as moonbody and sunbody, respectively, is introduced. These engineered antibody-like modular domains enable rapid and reversible antibody-antigen recognition by utilizing light. By the paralleled insertion of two light-oxygen-voltage domain 2 modules into a single sunbody and the use of bivalent sunbodies, the range of dynamic changes of photoswitchable sunbodies is substantially enhanced. Furthermore, the use of moonbodies or sunbodies to precisely control protein degradation, gene transcription, and base editing by harnessing the power of light is demonstrated.

| S-EPMC8295464 | biostudies-literature

Data for the synthesis of pyrogallol-formaldehyde aerogels using two acid catalysts oxalic acid y hydrochloric acid.

Project description:Aerogels are extremely porous materials with large pore volumes and low bulk densities. Their unique structure imparts extraordinary properties and wide applications. The synthesis of pyrogallol-formaldehyde xerogels has been reported using HClO4 as a catalyst, but according to the literature review the synthesis of aerogels of these materials has not been documented. In the present work, the data for the synthesis of aerogels pyrogallol-formaldehyde are presented using oxalic acid and hydrochloric acid as catalysts. Also includes the data of the characterization of these materials by Infrared spectroscopy, thermogravimetric analysis Tg-DTG, Physisorption of N2, Raman Spectroscopy, X-ray Diffraction (XRD) and Scanning Electron Microscopy (SEM). It was determined that the use of these precursors of the synthesis of aerogels in acid medium, leads to the obtaining of microporous solids with a high value of the surface area, the material with the highest value of this parameter has been CAePF OA550 at have a BET area value of 1066 m2 g-1.

| S-EPMC6660616 | biostudies-literature

Emissions Control of Hydrochloric and Fluorhydric Acid in cement Factories from Romania.

Project description:From the available statistical data, cement factories co-process a range of over 100 types of waste (sorted both industrial and household) being authorized for their use as combustion components in clinker ovens. Therefore, the level of emissions is different depending on the type of fuels and waste used. The amount of industrial and municipal co-processed waste in the Romanian cement industry from 2004 to 2013 was about 1,500,000 tons, the equivalent of municipal waste generated in a year for 18 cities with over 250,000 inhabitants. The objective of this paper was to evaluate the emission level of hydrochloric acid (HCl) and hydrofluoric acid (HF) at the clinker kilns at two cement factories in Romania for different annual time intervals and to do a comparative analysis, to estimate their compliance with legislation in force. The measurements results showed average emission levels of about 0.578 mg/Nm3 for HCl and about 0.100 mg/Nm3 for HF, in the first hours of the evening, but decreased at the beginning of the third tour, at about 0.385 mg/Nm3 for HCl, respectively, to about 0.085 mg/Nm3 for HF. The evolution of HCl and HF emission levels during the last 4 years showed a variable distribution of these acids.

| S-EPMC7037784 | biostudies-literature

Acute lung injury secondary to hydrochloric acid instillation induces small airway hyperresponsiveness.

Project description:BackgroundAcute respiratory distress syndrome (ARDS) is a severe form of respiratory failure characterized by altered lung mechanics and poor oxygenation. Bronchial hyperresponsiveness has been reported in ARDS survivors and animal models of acute lung injury. Whether this hyperreactivity occurs at the small airways or not is unknown.ObjectiveTo determine ex-vivo small airway reactivity in a rat model of acute lung injury (ALI) by hydrochloric acid (HCl) instillation.MethodsTwelve anesthetized rats were connected to mechanical ventilation for 4-hour, and randomly allocated to either ALI group (HCl intratracheal instillation; n=6) or Sham (intratracheal instillation of 0.9% NaCl; n=6). Oxygenation was assessed by arterial blood gases. After euthanasia, tissue samples from the right lung were harvested for histologic analysis and wet-dry weight ratio assessment. Precision cut lung slice technique (100-200 μm diameter) was applied in the left lung to evaluate ex vivo small airway constriction in response to histamine and carbachol stimulation, using phase-contrast video microscopy.ResultsRats from the ALI group exhibited hypoxemia, worse histologic lung injury, and increased lung wet-dry weight ratio as compared with the sham group. The bronchoconstrictor responsiveness was significantly higher in the ALI group, both for carbachol (maximal contraction of 84.5±2.5% versus 61.4±4.2% in the Sham group, P<0.05), and for histamine (maximal contraction of 78.6±5.3% versus 49.6±5.3% in the Sham group, P<0.05).ConclusionIn an animal model of acute lung injury secondary to HCL instillation, small airway hyperresponsiveness to carbachol and histamine is present. These results may provide further insight into the pathophysiology of ARDS.

| S-EPMC8661233 | biostudies-literature

Long-acting antibody ligand mimetics for HER4-selective agonism.

Project description:Neuregulin protein 1 (NRG1) is a large (>?60-amino-acid) natural peptide ligand for the ErbB protein family members HER3 and HER4. We developed an agonistic antibody modality, termed antibody ligand mimetics (ALM), by incorporating complex ligand agonists such as NRG1 into an antibody scaffold. We optimized the linker and ligand length to achieve native ligand activity in HEK293 cells and cardiomyocytes derived from induced pluripotent stem cells (iPSCs) and used a monomeric Fc-ligand fusion platform to steer the ligand specificity toward HER4-dominant agonism. With the help of selectivity engineering, these enhanced ALM molecules can provide an antibody scaffold with increased receptor specificity and the potential to greatly improve the pharmacokinetics, stability, and downstream developability profiles from the natural ligand approach. This ligand mimetic design and optimization approach can be expanded to apply to other cardiovascular disease targets and emerging therapeutic areas, providing differentiated drug molecules with increased specificity and extended half-life.

| S-EPMC7566517 | biostudies-literature

Pepsin-Containing Membranes for Controlled Monoclonal Antibody Digestion Prior to Mass Spectrometry Analysis.

Project description:Monoclonal antibodies (mAbs) are the fastest growing class of therapeutic drugs, because of their high specificities to target cells. Facile analysis of therapeutic mAbs and their post-translational modifications (PTMs) is essential for quality control, and mass spectrometry (MS) is the most powerful tool for antibody characterization. This study uses pepsin-containing nylon membranes as controlled proteolysis reactors for mAb digestion prior to ultrahigh-resolution Orbitrap MS analysis. Variation of the residence times (from 3 ms to 3 s) of antibody solutions in the membranes yields "bottom-up" (1-2 kDa) to "middle-down" (5-15 kDa) peptide sizes within less than 10 min. These peptides cover the entire sequences of Trastuzumab and a Waters antibody, and a proteolytic peptide comprised of 140 amino acids from the Waters antibody contains all three complementarity determining regions on the light chain. This work compares the performance of "bottom-up" (in-solution tryptic digestion), "top-down" (intact protein fragmentation), and "middle-down" (in-membrane digestion) analysis of an antibody light chain. Data from tandem MS show 99%, 55%, and 99% bond cleavage for "bottom-up", "top-down", and "middle-down" analyses, respectively. In-membrane digestion also facilitates detection of PTMs such as oxidation, deamidation, N-terminal pyroglutamic acid formation, and glycosylation. Compared to "bottom-up" and "top-down" approaches for antibody characterization, in-membrane digestion uses minimal sample preparation time, and this technique also yields high peptide and sequence coverage for the identification of PTMs.

| S-EPMC5016144 | biostudies-literature

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