A history of pepsin and related enzymes

Increased Susceptibility of Rousettus aegyptiacus Bats to Respiratory SARS-CoV-2 Challenge Despite Its Distinct Tropism for Gut Epithelia in Bats

Increasing evidence suggests bats are the ancestral hosts of the majority of coronaviruses. In general, coronaviruses primarily target the gastrointestinal system, while some strains, especially Betacoronaviruses with the most relevant representatives SARS-CoV, MERS-CoV, and SARS-CoV-2, also cause severe respiratory disease in humans and other mammals. We previously reported the susceptibility of Rousettus aegyptiacus (Egyptian fruit bats) to intranasal SARS-CoV-2 infection. Here, we compared their permissiveness to an oral infection versus respiratory challenge (intranasal or orotracheal) by assessing virus shedding, host immune responses, tissue-specific pathology, and physiological parameters. While respiratory challenge with a moderate infection dose of 1 × 104 TCID50 caused a systemic infection with oral and nasal shedding of replication-competent virus, the oral challenge only induced nasal shedding of low levels of viral RNA. Even after a challenge with a higher infection dose of 1 × 106 TCID50, no replication-competent virus was detectable in any of the samples of the orally challenged bats. We postulate that SARS-CoV-2 is inactivated by HCl and digested by pepsin in the stomach of R. aegyptiacus, thereby decreasing the efficiency of an oral infection. Therefore, fecal shedding of RNA seems to depend on systemic dissemination upon respiratory infection. These findings may influence our general understanding of the pathophysiology of coronavirus infections in bats.

Kallikrein-related peptidases: mechanistic understanding for potential therapeutic targeting in cancer

INTRODUCTION

Human kallikrein-related peptidases (KLKs) represent a subgroup of 15 serine endopeptidases involved in various physiological processes and pathologies, including cancer.

AREAS COVERED

This review aims to provide a comprehensive overview of the KLK family, highlighting their genomic structure, expression profiles and substrate specificity. We explore the role of KLKs in tumorigenesis, emphasizing their potential as biomarkers and therapeutic targets in cancer treatment. The dysregulated activity of KLKs has been linked to various malignancies, making them promising candidates for cancer diagnostics and therapy.

EXPERT OPINION

: Recent advancements in understanding the mechanistic pathways of KLK-related tumorigenesis offer new prospects for developing targeted cancer treatments. Expert opinion suggests that while significant progress has been made, further research is necessary to fully exploit KLKs' potential in clinical applications.

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.

Perspective on Agricultural Industrialization: Modification Strategies for Enhancing the Catalytic Capacity of Keratinase

Keratinases is a special hydrolytic enzyme produced by microorganisms, which has the ability to catalyze the degradation of keratin. Currently, keratinases show great potential for application in many agricultural and industrial fields, such as biofermented feed, leather tanning, hair removal, and fertilizer production. However, these potentials have not yet been fully unleashed on an industrial scale. This paper reviews the sources, properties, and catalytic mechanisms of keratinases. Strategies for the molecular modification of keratinases are summarized and discussed in terms of improving the substrate specificity, thermostability, and pH tolerance of keratinases. The modification strategies are also enriched by the introduction of immobilized enzymes and directed evolution. In addition, the selection of modification strategies when facing specific industrial applications is discussed and prospects are provided. We believe that this review serves as a reference for the future quest to extend the application of keratinases from the laboratory to industry.

Mechanisms of Digestive Enzyme Response to Acute Salinity Stress in Juvenile Yellowfin Tuna (Thunnus albacares)

This study investigates the effect of a sudden change in salinity for 48 h on the digestive enzyme activity of juvenile yellowfin tuna. The treatment included a control salinity of 32‱ in natural seawater and an experimental salinity of 29‱. Acute stress experiments were carried out on 72 juvenile yellowfin tuna (646.52 ± 66.32 g) for 48 h to determine changes in digestive enzyme activity in different intestinal sections over time (0 h, 12 h, 24 h, 48 h). The activities of pepsin, trypsin, α-amylase, lipase, and chymotrypsin in the digestive organs (stomach, foregut, and pyloric ceca) of juvenile yellowfin tuna were measured. Pepsin and pancreatic protease in the experimental group were significantly lower than in the control group (p < 0.05). α-amylase showed a fluctuating trend of decreasing and then increasing, and its activity trend was pyloric ceca > foregut > stomach. The lipase activity of gastric tissues decreased at the beginning and then increased, reaching a minimum at 24 h (2.74 ± 1.99 U·g protein-1). The change of lipase in the pyloric ceca and foregut was increasing and then decreasing. The lipase activity trend was pyloric ceca > foregut > stomach. The chymotrypsin showed a decreasing and increasing trend and then stabilized at 48 h with a pattern of pyloric ceca > foregut > stomach. Similarly, the gut villi morphology was not significantly altered in the acutely salinity-stressed compared to the non-salinity-stressed. This study suggests that salinity may change the digestive function of juvenile yellowfin tuna, thereby affecting fish feeding, growth, and development. On the contrary, yellowfin tuna is highly adapted to 29‱ salinity. However, excessive stress may negatively affect digestive enzyme activity and reduce fish digestibility. This study may provide a scientific basis for a coastal aquaculture water environment for yellowfin tuna farming, which may guide the development and cultivation of aquaculture.

Non-Canonical Amino Acids in Analyses of Protease Structure and Function

All known organisms encode 20 canonical amino acids by base triplets in the genetic code. The cellular translational machinery produces proteins consisting mainly of these amino acids. Several hundred natural amino acids serve important functions in metabolism, as scaffold molecules, and in signal transduction. New side chains are generated mainly by post-translational modifications, while others have altered backbones, such as the β- or γ-amino acids, or they undergo stereochemical inversion, e.g., in the case of D-amino acids. In addition, the number of non-canonical amino acids has further increased by chemical syntheses. Since many of these non-canonical amino acids confer resistance to proteolytic degradation, they are potential protease inhibitors and tools for specificity profiling studies in substrate optimization and enzyme inhibition. Other applications include in vitro and in vivo studies of enzyme kinetics, molecular interactions and bioimaging, to name a few. Amino acids with bio-orthogonal labels are particularly attractive, enabling various cross-link and click reactions for structure-functional studies. Here, we cover the latest developments in protease research with non-canonical amino acids, which opens up a great potential, e.g., for novel prodrugs activated by proteases or for other pharmaceutical compounds, some of which have already reached the clinical trial stage.

The roles of proteases in prostate cancer

Since the proposition of the pro-invasive activity of proteolytic enzymes over 70 years ago, several roles for proteases in cancer progression have been established. About half of the 473 active human proteases are expressed in the prostate and many of the most well-characterized members of this enzyme family are regulated by androgens, hormones essential for development of prostate cancer. Most notably, several kallikrein-related peptidases, including KLK3 (prostate-specific antigen, PSA), the most well-known prostate cancer marker, and type II transmembrane serine proteases, such as TMPRSS2 and matriptase, have been extensively studied and found to promote prostate cancer progression. Recent findings also suggest a critical role for proteases in the development of advanced and aggressive castration-resistant prostate cancer (CRPC). Perhaps the most intriguing evidence for this role comes from studies showing that the protease-activated transmembrane proteins, Notch and CDCP1, are associated with the development of CRPC. Here, we review the roles of proteases in prostate cancer, with a special focus on their regulation by androgens.

Phylogenetic and AlphaFold predicted structure analyses provide insights for A1 aspartic protease family classification in Arabidopsis

Aspartic proteases are widely distributed in animals, plants, fungi and other organisms. In land plants, A1 aspartic protease family members have been implicated to play important and varied roles in growth, development and defense. Thus a robust classification of this family is important for understanding their gene function and evolution. However, current A1 family members in Arabidopsis are less well classified and need to be re-evaluated. In this paper, 70 A1 aspartic proteases in Arabidopsis are divided into four groups (group I-IV) based on phylogenetic and gene structure analyses of 1200 A1 aspartic proteases which are obtained from 12 Embryophyta species. Group I-III members are further classified into 2, 4 and 7 subgroups based on the AlphaFold predicted structures. Furthermore, unique insights of A1 aspartic proteases have been unraveled by AlphaFold predicted structures. For example, subgroup II-C members have a unique II-C specific motif in the C-extend domain, and subgroup IV is a Spermatophyta conserved group without canonical DTGS/DSGT active sites. These results prove that AlphaFold combining phylogenetic analysis is a promising solution for complex gene family classification.

Molecular interaction of di-ester bonded cationic Gemini surfactants with pepsin: in vitro and in silico perspectives

The implications of surfactant-enzyme/protein interactions in a variety of fields, including biotechnology, cosmetics, paints and pharmaceuticals, have attracted a lot of attention in contemporary studies. Herein, we have employed several in vitro and in silico techniques such as excitation and absorption spectroscopies, circular dichroism and FT-IR spectroscopies, density functional and molecular dynamics simulations to understand the interaction behavior of oxy-diester-based green cationic Gemini surfactants, N1,N1,N14,N14-tetramethyl-2,13-dioxo-N1,N14-dialkyl-3,6,12-tetraoxateradecane-1,14-diaminiumdichloride (abbreviated as Cm-E2O2-Cm, where 'm' stands for alkyl chain length, m = 12 and 14) with one of the main digestive proteins, pepsin. The spectroscopic techniques confirm the static quenching effect of surfactants on pepsin. The calculated physical parameters (Ksv, Kb and ΔG) and their order reveal the distinguished implications for the surfactants' chain lengths. The spontaneity of interaction was also confirmed by negative Gibbs free energy change values. The extrinsic spectroscopic study with pyrene as fluorescence probe, FT-IR and CD techniques indicated a potential conformational change in pepsin induced by the Gemini surfactants. DFT, docking and MD simulations provided the theoretical understanding regarding the quantum mechanical environment, location of binding and stability of the protein-surfactant complexation in energy terms. We believe this study will be a humble addition to our existing knowledge in the field of protein-surfactant interactions.Communicated by Ramaswamy H. Sarma.

The digestive systems of carnivorous plants

To survive in the nutrient-poor habitats, carnivorous plants capture small organisms comprising complex substances not suitable for immediate reuse. The traps of carnivorous plants, which are analogous to the digestive systems of animals, are equipped with mechanisms for the breakdown and absorption of nutrients. Such capabilities have been acquired convergently over the past tens of millions of years in multiple angiosperm lineages by modifying plant-specific organs including leaves. The epidermis of carnivorous trap leaves bears groups of specialized cells called glands, which acquire substances from their prey via digestion and absorption. The digestive glands of carnivorous plants secrete mucilage, pitcher fluids, acids, and proteins, including digestive enzymes. The same (or morphologically distinct) glands then absorb the released compounds via various membrane transport proteins or endocytosis. Thus, these glands function in a manner similar to animal cells that are physiologically important in the digestive system, such as the parietal cells of the stomach and intestinal epithelial cells. Yet, carnivorous plants are equipped with strategies that deal with or incorporate plant-specific features, such as cell walls, epidermal cuticles, and phytohormones. In this review, we provide a systematic perspective on the digestive and absorptive capacity of convergently evolved carnivorous plants, with an emphasis on the forms and functions of glands.

Pepsin and pH of Gastric Juice in Patients With Gastrointestinal Reflux Disease and Subgroups

GOAL

The aim of this study was to investigate the pepsin values and pH results of gastric juice among the subtypes of gastroesophageal reflux disease (GERD) and functional heartburn.

BACKGROUND

The major destructive agents of GERD on the esophageal epithelium are gastric acid and pepsin. No precise information about pepsin concentration in gastric juice exists.

STUDY

Ninety patients with GERD, 39 erosive reflux disease (ERD) Los Angeles (LA) grade A/B, 13 ERD LA grade C/D, 19 nonerosive reflux disease (NERD), 8 esophageal hypersensitivity, 11 functional heartburn, and 24 healthy controls were included in the study. During endoscopy gastric juices from the patients were aspirated and their pH readings immediately recorded. Gastric juice samples were analyzed using Peptest, a lateral flow device containing 2 unique human monoclonal antibodies to detect any pepsin present in the gastric juice sample.

RESULTS

The highest mean gastric pepsin concentration (0.865 mg/mL) and the lowest median gastric pH (1.4) was observed in the LA grade C/D group compared with the lowest mean gastric pepsin concentration (0.576 mg/mL) and the highest median gastric pH (2.5) seen in the NERD group. Comparing pH, the NERD patient group was significantly higher (P=0.0018 to P=0.0233) when compared with all other GERD patient groups.

CONCLUSIONS

The basal gastric pepsin level in the healthy control group was comparable to literature values. There was good correlation and a significant linear relationship between the gastric pepsin level and gastric pH within the patient groups. The severity of the GERD disease is related to the lowest pH and the highest pepsin concentration in gastric juice.

A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values

Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.

Activation of dopamine D2 receptor promotes pepsinogen secretion by suppressing somatostatin release from the mouse gastric mucosa

In vivo administration of dopamine (DA) receptor (DR)-related drugs modulate gastric pepsinogen secretion. However, DRs on gastric pepsinogen-secreting chief cells and DA D2 receptor (D2R) on somatostatin-secreting D cells were subsequently acquired. In this study, we aimed to further investigate the local effect of DA on gastric pepsinogen secretion through DRs expressed on chief cells or potential D2Rs expressed on D cells. To elucidate the modulation of DRs in gastric pepsinogen secretion, immunofluorescence staining, ex vivo incubation of gastric mucosa isolated from normal and D2R-/- mice were conducted, accompanied by measurements of pepsinogen or somatostatin levels using biochemical assays or enzyme-linked immunosorbent assays. D1R, D2R, and D5R-immunoreactivity (IR) were observed on chief cells in mouse gastric mucosa. D2R-IR was widely distributed on D cells from the corpus to the antrum. Ex vivo incubation results showed that DA and the D1-like receptor agonist SKF38393 increased pepsinogen secretion, which was blocked by the D1-like receptor antagonist SCH23390. However, D2-like receptor agonist quinpirole also significantly increased pepsinogen secretion, and D2-like receptor antagonist sulpiride blocked the promotion of DA. Besides, D2-like receptors exerted an inhibitory effect on somatostatin secretion, in contrast to their effect on pepsinogen secretion. Furthermore, D2R-/- mice showed much lower basal pepsinogen secretion but significantly increased somatostatin release and an increased number of D cells in gastric mucosa. Only SKF38393, not quinpirole, increased pepsinogen secretion in D2R-/- mice. DA promotes gastric pepsinogen secretion directly through D1-like receptors on chief cells and indirectly through D2R-mediated suppression of somatostatin release.

Origin of Proteolytic Stability of Peptide-Brush Polymers as Globular Proteomimetics

Peptide-brush polymers (PBPs), wherein every side-chain of the polymers is peptidic, represent a new class of proteomimetic with unusually high proteolytic resistance while maintaining bioactivity. Here, we sought to determine the origin of this behavior and to assess its generality via a combined theory and experimental approach. A series of PBPs with various polymer backbone structures were prepared and examined for their proteolytic stability and bioactivity. We discovered that an increase in the hydrophobicity of the polymer backbones is predictive of an elevation in proteolytic stability of the side-chain peptides. Computer simulations, together with small-angle X-ray scattering (SAXS) analysis, revealed globular morphologies for these polymers, in which pendant peptides condense around hydrophobic synthetic polymer backbones driven by the hydrophobic effect. As the hydrophobicity of the polymer backbones increases, the extent of solvent exposure of peptide cleavage sites decreases, reducing their accessibility to proteolytic enzymes. This study provides insight into the important factors driving PBP aqueous-phase structures to behave as globular, synthetic polymer-based proteomimetics.

Protein Footprinting, Conformational Dynamics, and Core Interface-Adjacent Neutralization "Hotspots" in the SARS-CoV-2 Spike Protein Receptor Binding Domain/Human ACE2 Interaction

The novel severe respiratory syndrome-like coronavirus (SARS-CoV-2) causes COVID-19 in humans and is responsible for one of the most destructive pandemics of the last century. At the root of SARS-CoV infection is the interaction between the viral spike protein and the human angiotensin converting enzyme 2 protein, which allows the virus to gain entry into host cells through endocytosis. In this work, we apply hydrogen-deuterium exchange mass spectrometry (HDX-MS) to provide a detailed view of the functional footprint and conformational dynamics associated with this interaction. Our results broadly agree with the binding interface derived from high resolution X-ray crystal structure data but also provide insights into shifts in structure and dynamics that accompany complexation, including some that occur immediately outside of the core binding interface. We propose that dampening of these "binding-site adjacent" dynamic shifts could represent a mechanism for neutralizing activity in a multitude of spike protein-targeted mAbs that have been found to specifically bind these "peripheral" sites. Our results highlight the unique capacity of HDX-MS to detect potential neutralization "hotspots" outside of the core binding interfaces defined by high resolution structural data.

[Historical construction of the concept of the enzyme and approaches in biology textbooks]

The use of the history and philosophy of science in teaching and learning is commonly neglected, linear, and/or out of context in textbooks. This article investigates whether this also occurs with the concept of enzymes. A brief review of the literature establishes the theoretical foundation to investigate how the concept of enzymes is presented in nine textbooks, following three different lines of analysis. A general lack of interconnection was seen in biochemistry topics, with enzymes usually only presented via the "lock-and-key" model, which does not best represent their complexity. Furthermore, conceptual limitations resulting from a lack of historical contextualization (partial or complete) were also observed.

Recent advances in proteolytic stability for peptide, protein, and antibody drug discovery

Introduction: To discover and develop a peptide, protein, or antibody into a drug requires overcoming multiple challenges to obtain desired properties. Proteolytic stability is one of the challenges and deserves a focused investigation.Areas covered: This review concentrates on improving proteolytic stability by engineering the amino acids around the cleavage sites of a liable peptide, protein, or antibody. Peptidases are discussed on three levels including all peptidases in databases, mixtures based on organ and tissue types, and individual peptidases. The technique to identify cleavage sites is spotlighted on mass spectrometry-based approaches such as MALDI-TOF and LC-MS. For sequence engineering, the replacements that have been commonly applied with a higher chance of success are highlighted at the beginning, while the rarely used and more complicated replacements are discussed later. Although a one-size-fits-all approach does not exist to apply to different projects, this review provides a 3-step strategy for effectively and efficiently conducting the proteolytic stability experiments to achieve the eventual goal of improving the stability by engineering the molecule itself.Expert opinion: Improving the proteolytic stability is a spiraling up process sequenced by testing and engineering. There are many ways to engineer amino acids, but the choice must consider the cost and properties affected by the changes of the amino acids.

Constitutive expression of Camelus bactrianus prochymosin B in Pichia pastoris

Camel chymosin can be efficiently employed to produce cheese. Traditionally the rennet enzyme produced by the glands of the fourth stomach of ruminant animals (abomassum) is used in cheese making. Full-length Camelus bactrianus (Bactrian camel) prochymosin gene was synthesized and constitutively expressed in Pichia pastoris cells under glyceraldehydes-3-phosphate dehydrogenase (GAP) promoter. It was purified by sequential anion and cation exchange chromatography. SDS-PAGE analysis resulted in two bands, approximately 42 and 35 kDa. The 42 kDa band vanished when the sample was treated with endoglycosidase H, indicating that the recombinant protein is partially glycosylated. Optimal pH for the activity of the highest-purity recombinant chymosin was pH 4.5 for cow's milk and pH 4.0 for mare's milk. The range 45-50 °C and 70 °C for cow's and mare's milk types, respectively, was found to be the most appropriate for maximal relative milk-clotting activity. Concentration of CaCl2 that ensured the stability of the chymosin milk-clotting activity was between 20 and 50 mM with an optimum at 30 mM. Milk-clotting activity of camel recombinant chymosin and ability to make curd was successfully tested on fresh mare's milk. Pichia pastoris strain with integrated camel chymosin gene showed high productivity of submerged fermentation in bioreactor with milk-clotting activity 1412 U/mL and 80 mg/L enzyme yield. These results suggest that the constitutive expression of the camel chymosin Camelus bactrianus in the yeast Pichia pastoris has good prospects for practical applications.

Reductionism in the study of enzyme adaptation

One of the principal goals of comparative biology is the elucidation of mechanisms by which organisms adapt to different environments. The study of enzyme structure, function, and stability has contributed significantly to this effort, by revealing adaptation at a molecular level. Comparative biochemistry, including enzymology, necessarily pursues a reductionist approach in describing the function and structure of biomolecules, allowing more straightforward study of molecular systems by removing much of the complexity of their biological milieu. Although this reductionism has allowed a remarkable series of discoveries linking chemical processes to metabolism and to whole-organism function in the context of the environment, it also has the potential to mislead when careful consideration is not made of the simplifying assumptions inherent to such research. In this review, a brief history of the growth of enzymology, its reliance on a reductionist philosophy, and its contributions to our understanding of biological systems is given. Examples then are provided of research techniques, based on a reductionist approach, that have advanced our knowledge about enzyme adaptation to environmental stresses, including stability assays, enzyme kinetics, and the impact of solute composition on enzyme function. In each case, the benefits of the reductionist nature of the approach is emphasized, notable advances are described, but potential drawbacks due to inherent oversimplification of the study system are also identified.

Defense and Offense Strategies: The Role of Aspartic Proteases in Plant-Pathogen Interactions

Plant aspartic proteases (APs; E.C.3.4.23) are a group of proteolytic enzymes widely distributed among different species characterized by the conserved sequence Asp-Gly-Thr at the active site. With a broad spectrum of biological roles, plant APs are suggested to undergo functional specialization and to be crucial in developmental processes, such as in both biotic and abiotic stress responses. Over the last decade, an increasing number of publications highlighted the APs' involvement in plant defense responses against a diversity of stresses. In contrast, few studies regarding pathogen-secreted APs and AP inhibitors have been published so far. In this review, we provide a comprehensive picture of aspartic proteases from plant and pathogenic origins, focusing on their relevance and participation in defense and offense strategies in plant-pathogen interactions.

Cholesterol-lowering drugs the simvastatin and atorvastatin change the protease activity of pepsin: An experimental and computational study

In this study, the effect of long-term use drugs of cholesterol-lowering atorvastatin and simvastatin on the activity and molecular structure of pepsin as important gastric enzyme was investigated by various experimental and computational methods. Based on the results obtained from fluorescence experiments, both drugs can bond to pepsin and quench the fluorescence intensity of protein through the static quenching mechanism. Also analysis of the thermodynamic parameters of binding the drugs to pepsin showed that the main forces in the complex formation for both are hydrophobic interactions and van der Waals forces. The effects of the drugs on the enzymatic activity of pepsin were then investigated and results showed that in the presence of both drugs the catalytic activity of the enzyme was significantly increased in lower (0.3-0.6 mM) concentrations however about the atorvastatin, increasing the concentration (0.9 mM) decreased the protease activity of pepsin. Also as a result of the FTIR studies, it was found that binding of the drugs to protein did not significant alteration in the structure of the protein. In order to obtain the atomic details of drug-protein interactions, the computational calculations were performed. The results in good agreement with those obtained from the experimental for interaction; confirm that the drugs both are bind to a cleft near the active site of the protein without any change in the structure of pepsin. Overall from the results obtained in this study, it can be concluded that both simvastatin and atorvastatin can strongly bond to a location close to the active site of pepsin and the binding change the enzymatic activity of protein.

Optimization and Pretreatment for Hot Water Extraction of Korean Deer (Cervus canadensis Erxleben) Velvet Antlers

Velvet antler (VA) is a historically traditional medicinal supplement and is well known in Asian countries for its pharmaceutical and health benefits. The objectives for this study were to optimize the hot water extraction (HWE) of VA for the Korean VA industry, and to determine the most effective pretreatment method among microwave (MW), ultrasonication (US), and enzymatic (EZ) techniques. Using response surface methodology, optimum extraction temperatures and times were determined by central composite design configuration based on extraction yield and sialic acid content. Various quality parameters of VA extract including yield, soluble solid, protein, and sialic acid contents were also compared with the conjunction of HWE and pretreatment. The yield and sialic acid content of VA extract were determined to be 40% and 0.73 mg/g, respectively, under an optimum temperature of 100°C at 24 h of extraction time. The yields from VA extracts pretreated with MW, US, and EZ were 17.42%, 19.73%, and 29.15%, respectively. Among the tested commercial enzymes, pepsin was the most effective proteolytic enzyme and led to the highest yield (47.65%), soluble solids (4.03 °brix), protein (1.12 mg/ml), and sialic acid (3.04 mg/ml) contents from VA extract.

Production of F(ab')2 from Monoclonal and Polyclonal Antibodies

Antibodies are widely used in therapeutic, diagnostic, and research applications, and antibody derivatives such as F(ab')₂ fragments are used when only a particular antibody region is required. F(ab')₂ can be produced through antibody engineering, but some applications require F(ab')₂ produced from an original formulated antibody or directly from a polyclonal antibody pool. The cysteine protease immunoglobulin-degrading enzyme (IdeS) from Streptococcus pyogenes digests immunoglobulin G (IgG) specifically and efficiently to produce F(ab')₂ . Here we detail the production and purification of recombinant IdeS; its utilization to digest monoclonal or polyclonal antibodies to F(ab')₂ fragments; and F(ab')₂ purification through consecutive affinity chromatography steps. The resultant F(ab')₂ exhibit high purity, retain antigen-binding functionality, and are readily utilizable in various downstream applications. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Production and purification of F(ab')₂ fragments from monoclonal and polyclonal antibodies using IdeS Alternate Protocol: Purification of polyclonal antigen-specific F(ab')₂ fragments from human serum or secretions Support Protocol: Production and purification of IdeS.

Effect of fermented milk from Lactococcus lactis ssp. cremoris strain JFR1 on Salmonella invasion of intestinal epithelial cells

The process of fermentation contributes to the organoleptic properties, preservation, and nutritional benefits of food. Fermented food may interfere with pathogen infections through a variety of mechanisms, including competitive exclusion or improving intestinal barrier integrity. In this study, the effect of milk fermented with Lactococcus lactis ssp. cremoris JFR1 on Salmonella invasion of intestinal epithelial cell cultures was investigated. Epithelial cells (HT29-MTX, Caco-2, and cocultures of the 2) were treated for 1 h with Lactococcus lactis ssp. cremoris JFR1 fermented milk before infection with Salmonella enterica ssp. enterica Typhimurium. Treatment with fermented milk resulted in increased transepithelial electrical resistance, which remained constant for the duration of infection (up to 3 h), illustrating a protective effect. After gentamicin treatment to remove adhered bacterial cells, enumeration revealed a reduction in numbers of intracellular Salmonella. Quantitative reverse-transcription PCR data indicated a downregulation of Salmonella virulence genes hilA, invA, and sopD after treatment with fermented milk. Fermented milk treatment of epithelial cells also exhibited an immunomodulatory effect reducing the production of proinflammatory IL-8. In contrast, chemically acidified milk (glucono delta-lactone) failed to show the same effect on monolayer integrity, Salmonella Typhimurium invasion, and gene expression as well as immune modulation. Furthermore, an oppA knockout mutant of Salmonella Typhimurium infecting treated epithelial cells did not show suppressed virulence gene expression. Collectively, these results suggest that milk fermented with Lactococcus lactis ssp. cremoris JFR1 is effective in vitro in the reduction of Salmonella invasion into intestinal epithelial cells. A functional OppA permease in Salmonella is required to obtain the antivirulence effect of fermented milk.

An n→π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole

Aspartic proteases regulate many biological processes and are prominent targets for therapeutic intervention. Structural studies have captured intermediates along the reaction pathway, including the Michaelis complex and tetrahedral intermediate. Using a Ramachandran analysis of these structures, we discovered that residues occupying the P1 and P1' positions (which flank the scissile peptide bond) adopt the dihedral angle of an inverse γ-turn and polyproline type-II helix, respectively. Computational analyses reveal that the polyproline type-II helix engenders an n→π* interaction in which the oxygen of the scissile peptide bond is the donor. This interaction stabilizes the negative charge that develops in the tetrahedral intermediate, much like the oxyanion hole of serine proteases. The inverse γ-turn serves to twist the scissile peptide bond, vacating the carbonyl π* orbital and facilitating its hydration. These previously unappreciated interactions entail a form of substrate-assisted catalysis and offer opportunities for drug design.

Proteases: Pivot Points in Functional Proteomics

Proteases drive the life cycle of all proteins, ensuring the transportation and activation of newly minted, would-be proteins into their functional form while recycling spent or unneeded proteins. Far from their image as engines of protein digestion, proteases play fundamental roles in basic physiology and regulation at multiple levels of systems biology. Proteases are intimately associated with disease and modulation of proteolytic activity is the presumed target for successful therapeutics. "Proteases: Pivot Points in Functional Proteomics" examines the crucial roles of proteolysis across a wide range of physiological processes and diseases. The existing and potential impacts of proteolysis-related activity on drug and biomarker development are presented in detail. All told the decisive roles of proteases in four major categories comprising 23 separate subcategories are addressed. Within this construct, 15 sets of subject-specific, tabulated data are presented that include identification of proteases, protease inhibitors, substrates, and their actions. Said data are derived from and confirmed by over 300 references. Cross comparison of datasets indicates that proteases, their inhibitors/promoters and substrates intersect over a range of physiological processes and diseases, both chronic and pathogenic. Indeed, "Proteases: Pivot Points …" closes by dramatizing this very point through association of (pro)Thrombin and Fibrin(ogen) with: hemostasis, innate immunity, cardiovascular and metabolic disease, cancer, neurodegeneration, and bacterial self-defense.

Pepsin: biomarker, mediator, and therapeutic target for reflux and aspiration

Extra-esophageal reflux is suspected to cause a wide range of clinical symptoms in the upper airways. Diagnosis and treatment has focused on acid, but realization of the role of nonacid reflux has resulted in research investigating the use of pepsin as a biomarker for gastric reflux and aspiration. Pepsin analysis can complement the use of questionnaires and office-based diagnosis and lessen the dependency on invasive and expensive diagnostic tests. Furthermore, pepsin as a first-line diagnostic biomarker has been shown to improve the accuracy of reflux diagnosis. In addition to its use as a diagnostic biomarker, pepsin has been shown to cause inflammation independent of the pH of the refluxate and thus despite acid suppression therapy. Research is ongoing to develop new therapies for airway reflux that specifically target pepsin.

Enzymatic treatment of pork protein for the enhancement of iron bioavailability

The typical intervention for iron-deficiency anaemia is through oral supplementation with iron salts, which have unpleasant side effects. Therefore, there is a need for the development of supplements which will be absorbed more effectively and may have fewer side effects. This study investigated the effects of partially hydrolysed pork proteins on the bioavailability of non-haem iron. The peptides were derived using either pepsin or a combination of bacterial and fungal proteases, and their ability to deliver iron was evaluated in a rat intestine epithelial tissue model. The greatest iron absorption was achieved with peptides hydrolysed by pepsin of low molecular weight (<6-8 kDa). The peptides hydrolysed with bacterial and fungal enzymes may have bound to the iron too strongly, affecting bioavailability. Finally, hydrolysing proteins using pepsin in the presence of iron produces a complex that resulted in more ferritin expression than mixing the peptides with iron after hydrolysis.

Mutacin 1140 Lantibiotic Variants Are Efficacious Against Clostridium difficile Infection

Lantibiotics offer an untapped pipeline for the development of novel antibiotics to treat serious Gram-positive (+) infections including Clostridium difficile. Mutacin 1140 (MU1140) is a lantibiotic produced by Streptococcus mutans and acts via a novel mechanism of action, which may limit the development of resistance. This study sought to identify a lead compound for the treatment of C. difficile associated diarrhea (CDAD). Compounds were selected from a saturation mutagenesis library of 418 single amino acid variants of MU1140. Compounds were produced by small scale fermentation, purified, characterized and then subjected to a panel of assays aimed at identifying the best performers. The screening assays included: in vitro susceptibility testing [MIC against Micrococcus luteus, Clostridium difficile, vancomycin-resistant enterococci (VRE), Staphylococcus aureus, Streptococcus pneumonia, Mycobacterium phlei, and Pseudomonas aeruginosa; cytotoxicity screening on HepG2 hepatocytes; in vitro pharmacological profiling with the Safety Screen 44^TM, metabolic and chemical stability in biologically relevant fluids (FaSSGF, FaSSIF and serum); and efficacy in vivo]. Several lantibiotic compounds had better MIC against C. difficile, compared to vancomycin, but not against other bacterial species tested. The Safety Screen 44^TMin vitro pharmacological profiling assay suggested that this class of compounds has relatively low overall toxicity and that compound OG253 (MU1140, Phe1Ile) is not likely to present inadvertent off-target effects, as evidenced by a low promiscuity score. The in vitro cytotoxicity assay also indicated that this class of compounds was characterized by low toxicity; the EC₅₀ of OG253 was 636 mg/mL on HepG2 cells. The half-life in simulated gastric fluid was >240 min. for all compound tested. The stability in simulated intestinal fluid ranged between a half-life of 5 min to >240 min, and paralleled the half-life in serum. OG253 ultimately emerged as the lead compound based on superior in vivo efficacy along with an apparent lack of relapse in a hamster model of infection. The lessons learned from this report are applicable to therapeutic lanthipeptides in general and may assist in the design of novel molecules with improved pharmacological, therapeutic and physicochemical profiles. The data presented also support the continued clinical development of OG253 as a novel antibiotic against CDAD that could prevent recurrence of the infection.

The Intrinsic Pepsin Resistance of Interleukin-8 Can Be Explained from a Combined Bioinformatical and Experimental Approach

Interleukin-8 (IL-8, CXCL8) is a neutrophil chemotactic factor belonging to the family of chemokines. IL-8 was shown to resist pepsin cleavage displaying its high resistance to this protease. However, the molecular mechanisms underlying this resistance are not fully understood. Using our in-house database containing the data on three-dimensional arrangements of secondary structure elements from the whole Protein Data Bank, we found a striking structural similarity between IL-8 and pepsin inhibitor-3. Such similarity could play a key role in understanding IL-8 resistance to the protease pepsin. To support this hypothesis, we applied pepsin assays confirming that intact IL-8 is not degraded by pepsin in comparison to IL-8 in a denaturated state. Applying ¹H-¹⁵N Heteronuclear Single Quantum Coherence NMR measurements, we determined the putative regions at IL-8 that are potentially responsible for interactions with the pepsin. The results obtained in this work contribute to the understanding of the resistance of IL-8 to pepsin proteolysis in terms of its structural properties.

Comparative genomic and plasmid analysis of beer-spoiling and non-beer-spoiling Lactobacillus brevis isolates

Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.

Sorghum-cowpea composite porridge as a functional food, Part II: Antioxidant properties as affected by simulated in vitro gastrointestinal digestion

The effect of compositing red non-tannin sorghum with brownish-cream cowpea and in vitro gastrointestinal digestion on total phenolic and flavonoid contents and antioxidant properties of a sorghum-cowpea composite porridge was studied. Maize-soybean composite porridge was used as a reference sample. Antioxidant properties were studied using radical scavenging activities against the 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid), peroxyl and NO radicals as well as inhibition of low density lipoprotein (LDL) oxidation and oxidative damage of vector DNA. Hydroperoxide content of the samples was also measured. All the samples demonstrated radical scavenging activity. Simulated duodenal digests of the porridges had hydroperoxides and therefore caused LDL oxidation. The undigested porridges and simulated gastric digests inhibited LDL oxidation. Compositing the cereals with legumes increased total phenolic and flavonoid contents and NO scavenging activity of their porridges. In vitro gastrointestinal digestion of the porridges increased their total phenolic and flavonoid contents, radical scavenging activities and LDL oxidation inhibitory activity.

Binding performance of pepsin surface-imprinted polymer particles in protein mixtures

Surface-imprinted polymer particles facilitate the accessibility of synthetic selective binding sites for proteins. Given their volume-to-surface ratio, submicron particles offer a potentially large surface area facilitating fast rebinding kinetics and high binding capacities, as investigated herein by batch rebinding experiments. Polymer particles were prepared with (3-acrylamidopropyl)trimethylammonium chloride as functional monomer, and ethylene glycol dimethacrylate as cross-linker in the presence of pepsin as template molecule via miniemulsion polymerization. The obtained polymer particles had an average particle diameter of 623 nm, and a specific surface area of 50 m² g^-1. The dissociation constant and maximum binding capacity were obtained by fitting the Langmuir equation to the corresponding binding isotherm. The dissociation constant was 7.94 μM, thereby indicating a high affinity; the binding capacity was 0.72 μmol m^-2. The binding process was remarkably fast, as equilibrium binding was observed after just 1 min of incubation. The previously determined selectivity of the molecularly imprinted polymer for pepsin was for the first time confirmed during competitive binding studies with pepsin, bovine serum albumin, and β-lactoglobulin. Since pepsin has an exceptionally high content in acidic amino acids enabling strong interactions with positively charged quaternary ammonium groups of the functional monomers, another competitive protein, i.e., α1-acid glycoprotein, was furthermore introduced. This protein has a similarly high content in acidic amino acids, and was used for demonstrating the implications of ionic interactions on the achieved selectivity.

Advanced Evaluation Strategies for Protein-Imprinted Polymer Nanobeads

Molecularly imprinted polymers (MIPs) are synthetic affinity matrices capable of selective binding a specific target molecule. A strategy for competitive selectivity studies is developed providing information on the selective binding properties of MIPs in complex matrices. Batch rebinding experiments entail the target protease, two other proteins, and MIP nanobeads. The protease is inhibited by addition of pepstatin thus quenching the degradation of the other proteins. The proteins are analyzed via sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The relevance of competitive selectivity studies for the evaluation of MIP performance is further emphasized by comparison to single protein rebinding experiments.

Analytical Aspects of Hydrogen Exchange Mass Spectrometry

This article reviews the analytical aspects of measuring hydrogen exchange by mass spectrometry (HX MS). We describe the nature of analytical selectivity in hydrogen exchange, then review the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in HX MS depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that can be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics.

Aspartic peptidases of human pathogenic trypanosomatids: perspectives and trends for chemotherapy

Aspartic peptidases are proteolytic enzymes present in many organisms like vertebrates, plants, fungi, protozoa and in some retroviruses such as human immunodeficiency virus (HIV). These enzymes are involved in important metabolic processes in microorganisms/virus and play major roles in infectious diseases. Although few studies have been performed in order to identify and characterize aspartic peptidase in trypanosomatids, which include the etiologic agents of leishmaniasis, Chagas’ disease and sleeping sickness, some beneficial properties of aspartic peptidase inhibitors have been described on fundamental biological events of these pathogenic agents. In this context, aspartic peptidase inhibitors (PIs) used in the current chemotherapy against HIV (e.g., amprenavir, indinavir, lopinavir, nelfinavir, ritonavir and saquinavir) were able to inhibit the aspartic peptidase activity produced by different species of Leishmania. Moreover, the treatment of Leishmania promastigotes with HIV PIs induced several perturbations on the parasite homeostasis, including loss of the motility and arrest of proliferation/growth. The HIV PIs also induced an increase in the level of reactive oxygen species and the appearance of irreversible morphological alterations, triggering parasite death pathways such as programed cell death (apoptosis) and uncontrolled autophagy. The blockage of physiological parasite events as well as the induction of death pathways culminated in its incapacity to adhere, survive and escape of phagocytic cells. Collectively, these results support the data showing that parasites treated with HIV PIs have a significant reduction in the ability to cause in vivo infection. Similarly, the treatment of Trypanosoma cruzi cells with pepstatin A showed a significant inhibition on both aspartic peptidase activity and growth as well as promoted several and irreversible morphological changes. These studies indicate that aspartic peptidases can be promising targets in trypanosomatid cells and aspartic proteolytic inhibitors can be benefic chemotherapeutic agents against these human pathogenic microorganisms.