Multiplexed Native Mass Spectrometry Determination of Ligand Selectivity for Fatty Acid-Binding Proteins.

Although multiple approaches for characterizing protein-ligand interactions are available in target-based drug discovery, their throughput for determining selectivity is quite limited. Herein, we describe the application of native mass spectrometry for rapid, multiplexed screening of the selectivity of eight small-molecule ligands for five fatty acid-binding protein isoforms. Using high-resolution mass spectrometry, we were able to identify and quantify up to 20 different protein species in a single spectrum. We show that selectivity profiles generated by native mass spectrometry are in good agreement with those of traditional solution-phase techniques such as isothermal titration calorimetry and fluorescence polarization. Furthermore, we propose strategies for effective investigation of selectivity by native mass spectrometry, thus highlighting the potential of this technique to be used as an orthogonal method to traditional biophysical approaches for rapid, multiplexed screening of protein-ligand complexes.

Fluoromethylketone-Fragment Conjugates Designed as Covalent Modifiers of EcDsbA are Atypical Substrates.

Disulfide bond protein A (DsbA) is an oxidoreductase enzyme that catalyzes the formation of disulfide bonds in Gram-negative bacteria. In Escherichia coli, DsbA (EcDsbA) is essential for bacterial virulence, thus inhibitors have the potential to act as antivirulence agents. A fragment-based screen was conducted against EcDsbA and herein we describe the development of a series of compounds based on a phenylthiophene hit identified from the screen. A novel thiol reactive and "clickable" ethynylfluoromethylketone was designed for reaction with azide-functionalized fragments to enable rapid and versatile attachment to a range of fragments. The resulting fluoromethylketone conjugates showed selectivity for reaction with the active site thiol of EcDsbA, however unexpectedly, turnover of the covalent adduct was observed. A mechanism for this turnover was investigated and proposed which may have wider ramifications for covalent reactions with dithiol-disulfide oxidoreducatases.

Canola Seed Protein: Pretreatment, Extraction, Structure, Physicochemical and Functional Characteristics.

The rapid growth of the global population has led to an unprecedented demand for dietary protein. Canola seeds, being a widely utilized oil resource, generate substantial meal by-products following oil extraction. Fortunately, canola meals are rich in protein. In this present review, foremost attention is directed towards summarizing the characteristics of canola seed and canola seed protein. Afterwards, points of discussion related to pretreatment include an introduction to pulsed electric field treatment (PEF), microwave treatment (MC), and ultrasound treatment (UL). Then, the extraction method is illustrated, including alkaline extraction, isoelectric precipitation, acid precipitation, micellization (salt extraction), and dry fractionation and tribo-electrostatic separation. Finally, the structural complexity, physicochemical properties, and functional capabilities of rapeseed seeds, as well as the profound impact of various applications of rapeseed proteins, are elaborated. Through a narrative review of recent research findings, this paper aims to enhance a comprehensive understanding of the potential of canola seed protein as a valuable nutritional supplement, highlighting the pivotal role played by various extraction methods. Additionally, it sheds light on the broad spectrum of applications where canola protein demonstrates its versatility and indispensability as a resource.

Rapid Elaboration of Fragments into Leads Applied to Bromodomain-3 Extra-Terminal Domain.

The development of low-affinity fragment hits into higher-affinity leads is a major hurdle in fragment-based drug design. Here, we demonstrate the Rapid Elaboration of Fragments into Leads (REFiL) by applying an integrated workflow that provides a systematic approach to generate higher-affinity binders without the need for structural information. The workflow involves the selection of commercial analogues of fragment hits to generate preliminary structure-activity relationships. This is followed by parallel microscale chemistry using chemoinformatically designed reagent libraries to rapidly explore chemical diversity. After a fragment screen against bromodomain-3 extra-terminal (BRD3-ET) domain, we applied the REFiL workflow, which allowed us to develop a series of ligands that bind to BRD3-ET. With REFiL, we were able to rapidly improve binding affinity > 30-fold. REFiL can be applied readily to a broad range of proteins without the need for a structure, allowing the efficient evolution of low-affinity fragments into higher-affinity leads and chemical probes.

Fragment screening libraries for the identification of protein hot spots and their minimal binding pharmacophores.

Fragment-based drug design relies heavily on structural information for the elaboration and optimisation of hits. The ability to identify neighbouring binding hot spots, energetically favourable interactions and conserved binding motifs in protein structures through X-ray crystallography can inform the evolution of fragments into lead-like compounds through structure-based design. The composition of fragment libraries can be designed and curated to fit this purpose and herein, we describe and compare screening libraries containing compounds comprising between 2 and 18 heavy atoms. We evaluate the properties of the compounds in these libraries and assess their ability to probe protein surfaces for binding hot spots.

Microemulsion: a novel alternative technique for edible oil extraction_a mechanistic viewpoint.

Microemulsions, as isotropic, transparent, nano size (<100 nm), and thermodynamically stable dispersions, are potentially capable of being used in food formulations, functional foods, pharmaceuticals, and in many other fields for various purposes, particularly for nano-encapsulation, extraction of bioactive compounds and oils, and as nano-reactors. However, their functionalities, and more importantly their oil extraction capability, strongly depend on, and are determined by, their formulation, molecular structures and the type, ratio and functionality of surfactants and co-surfactants. This review extensively describes microemulsions (definition, fabrication, thermodynamic aspects, and applications), and their various mechanisms of oil extraction (roll-up, snap-off, and solubilization including those by Winsor Types I, II, III, and IV systems). Applications of various food grade (natural or synthetic) and extended surfactants for edible oil extraction are then covered based on these concepts.

Improved Extraction Efficiency and Antioxidant Activity of Defatted Canola Meal Extract Phenolic Compounds Obtained from Air-Fried Seeds.

This study investigated the efficacy of roasting pre-treatment by air frying to enhance the extraction and recovery of the predominant sinapic acid derivatives (SADs) from roasted canola meal and the antioxidant potential of the methanolic extracts. Canola meal was obtained by air frying canola seed at 160, 170, 180 or 190 °C for 5, 10, 15 or 20 min. Oil was extracted using the Soxhlet method, and the de-oiled meal fraction was air-dried. Phenolic compounds were isolated using ultrasound-assisted extraction with 70% (v/v) methanol and then quantified by high-performance liquid chromatography-diode array detection. The antioxidant potential of the defatted meal methanolic extracts was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH), ferric reducing antioxidant power (FRAP), and metal ion-chelating activity (MIC) assays. The highest total phenolic content of 3.15 mg gallic acid equivalent/g dry weight was recorded in the defatted meal extract from seeds pre-treated with air frying at 190 °C for 15 min. Sinapine, sinapic acid and an unknown compound at a retention time (RT) of 26.6 min were the major sinapates identified in the defatted meal with the highest concentrations of 7572 ± 479.2 µg/g DW, 727 ± 43.45 µg/g DW and 1763 ± 73.5 µg/g DW, respectively, obtained at 160 °C for 5 min. Canolol (151.35 ± 7.65 µg/g DW) was detected after air frying at a temperature of 170 °C for 20 min. The FRAP and MIC correlated positively (r = 0.85) and generally decreased with increased air frying temperature-time conditions. The highest FRAP and MIC values of 0.53 mM and 80% were obtained at 160 °C for 5 and 20 min, respectively. The outcome of this study will contribute new knowledge that could improve the value addition and by-product utilization of canola seeds.

Relationship between nitrogen functionality and wheat flour dough rheology: Extensional and shear approaches.

Nitrogen supplied to wheat crops to increase grain productivity is being scrutinized because of its role in greenhouse gas emissions. Nitrogen affects food quality as well as food security because it increases grain protein content and can change wheat protein composition, both of which affect the rheological properties of dough made from the grain. This review explores the relationship between nitrogen functionality, wheat protein content and the ratio of gliadins to glutenins through critical assessment of recent studies on nitrogen fertilization of wheat. Moreover, by studying how variations in protein content and the gliadins/glutenins ratio affect the shear and extensional rheological properties of the dough, this review elucidates the direct role of nitrogen on wheat flour dough behavior during processing because process operations primarily employ extensional and shear forces. Nitrogen uptake by wheat plants leads to an increase in wheat protein content and changes in the gliadins/glutenins ratio. Confounding factors associated with wheat plant growth and dough preparation make it difficult to definitively separate effects of wheat protein content from effects of wheat protein composition on dough rheology. Nevertheless, in general, higher protein content is associated with larger gliadins/glutenins ratios, resulting in wheat flour doughs that are more extensible.

Methyl probes in proteins for determining ligand binding mode in weak protein-ligand complexes.

Structures of protein-ligand complexes provide critical information for drug design. Most protein-ligand complex structures are determined using X-ray crystallography, but where crystallography is not able to generate a structure for a complex, NMR is often the best alternative. However, the available tools to enable rapid and robust structure determination of protein-ligand complexes by NMR are currently limited. This leads to situations where projects are either discontinued or pursued without structural data, rendering the task more difficult. We previously reported the NMR Molecular Replacement (NMR2) approach that allows the structure of a protein-ligand complex to be determined without requiring the cumbersome task of protein resonance assignment. Herein, we describe the NMR2 approach to determine the binding pose of a small molecule in a weak protein-ligand complex by collecting sparse protein methyl-to-ligand NOEs from a selectively labeled protein sample and an unlabeled ligand. In the selective labeling scheme all methyl containing residues of the protein are protonated in an otherwise deuterated background. This allows measurement of intermolecular NOEs with greater sensitivity using standard NOESY pulse sequences instead of isotope-filtered NMR experiments. This labelling approach is well suited to the NMR2 approach and extends its utility to include larger protein-ligand complexes.

Novel small molecules that increase the susceptibility of Neisseria gonorrhoeae to cationic antimicrobial peptides by inhibiting lipid A phosphoethanolamine transferase.

OBJECTIVES: Neisseria gonorrhoeae is an exclusively human pathogen that commonly infects the urogenital tract resulting in gonorrhoea. Empirical treatment of gonorrhoea with antibiotics has led to multidrug resistance and the need for new therapeutics. Inactivation of lipooligosaccharide phosphoethanolamine transferase A (EptA), which attaches phosphoethanolamine to lipid A, results in attenuation of the pathogen in infection models. Small molecules that inhibit EptA are predicted to enhance natural clearance of gonococci via the human innate immune response. METHODS: A library of small-fragment compounds was tested for the ability to enhance susceptibility of the reference strain N. gonorrhoeae FA1090 to polymyxin B. The effect of these compounds on lipid A synthesis and viability in models of infection were tested. RESULTS: Three compounds, 135, 136 and 137, enhanced susceptibility of strain FA1090 to polymyxin B by 4-fold. Pre-treatment of bacterial cells with all three compounds resulted in enhanced killing by macrophages. Only lipid A from bacterial cells exposed to compound 137 showed a 17% reduction in the level of decoration of lipid A with phosphoethanolamine by MALDI-TOF MS analysis and reduced stimulation of cytokine responses in THP-1 cells. Binding of 137 occurred with higher affinity to purified EptA than the starting material, as determined by 1D saturation transfer difference NMR. Treatment of eight MDR strains with 137 increased susceptibility to polymyxin B in all cases. CONCLUSIONS: Small molecules have been designed that bind to EptA, inhibit addition of phosphoethanolamine to lipid A and can sensitize N. gonorrhoeae to killing by macrophages.

Selective Binding of Small Molecules to Vibrio cholerae DsbA Offers a Starting Point for the Design of Novel Antibacterials.

DsbA enzymes catalyze oxidative folding of proteins that are secreted into the periplasm of Gram-negative bacteria, and they are indispensable for the virulence of human pathogens such as Vibrio cholerae and Escherichia coli. Therefore, targeting DsbA represents an attractive approach to control bacterial virulence. X-ray crystal structures reveal that DsbA enzymes share a similar fold, however, the hydrophobic groove adjacent to the active site, which is implicated in substrate binding, is shorter and flatter in the structure of V. cholerae DsbA (VcDsbA) compared to E. coli DsbA (EcDsbA). The flat and largely featureless nature of this hydrophobic groove is challenging for the development of small molecule inhibitors. Using fragment-based screening approaches, we have identified a novel small molecule, based on the benzimidazole scaffold, that binds to the hydrophobic groove of oxidized VcDsbA with a KD of 446±10 µM. The same benzimidazole compound has ∼8-fold selectivity for VcDsbA over EcDsbA and binds to oxidized EcDsbA, with KD >3.5 mM. We generated a model of the benzimidazole complex with VcDsbA using NMR data but were unable to determine the structure of the benzimidazole bound EcDsbA using either NMR or X-ray crystallography. Therefore, a structural basis for the observed selectivity is unclear. To better understand ligand binding to these two enzymes we crystallized each of them in complex with a known ligand, the bile salt sodium taurocholate. The crystal structures show that taurocholate adopts different binding poses in complex with VcDsbA and EcDsbA, and reveal the protein-ligand interactions that stabilize the different modes of binding. This work highlights the capacity of fragment-based drug discovery to identify inhibitors of challenging protein targets. In addition, it provides a starting point for development of more potent and specific VcDsbA inhibitors that act through a novel anti-virulence mechanism.

Identification and characterization of two drug-like fragments that bind to the same cryptic binding pocket of Burkholderia pseudomallei DsbA.

Disulfide-bond-forming proteins (Dsbs) play a crucial role in the pathogenicity of many Gram-negative bacteria. Disulfide-bond-forming protein A (DsbA) catalyzes the formation of the disulfide bonds necessary for the activity and stability of multiple substrate proteins, including many virulence factors. Hence, DsbA is an attractive target for the development of new drugs to combat bacterial infections. Here, two fragments, bromophenoxy propanamide (1) and 4-methoxy-N-phenylbenzenesulfonamide (2), were identified that bind to DsbA from the pathogenic bacterium Burkholderia pseudomallei, the causative agent of melioidosis. The crystal structures of oxidized B. pseudomallei DsbA (termed BpsDsbA) co-crystallized with 1 or 2 show that both fragments bind to a hydrophobic pocket that is formed by a change in the side-chain orientation of Tyr110. This conformational change opens a `cryptic' pocket that is not evident in the apoprotein structure. This binding location was supported by 2D-NMR studies, which identified a chemical shift perturbation of the Tyr110 backbone amide resonance of more than 0.05 p.p.m. upon the addition of 2 mM fragment 1 and of more than 0.04 p.p.m. upon the addition of 1 mM fragment 2. Although binding was detected by both X-ray crystallography and NMR, the binding affinity (Kd) for both fragments was low (above 2 mM), suggesting weak interactions with BpsDsbA. This conclusion is also supported by the crystal structure models, which ascribe partial occupancy to the ligands in the cryptic binding pocket. Small fragments such as 1 and 2 are not expected to have a high energetic binding affinity due to their relatively small surface area and the few functional groups that are available for intermolecular interactions. However, their simplicity makes them ideal for functionalization and optimization. The identification of the binding sites of 1 and 2 to BpsDsbA could provide a starting point for the development of more potent novel antimicrobial compounds that target DsbA and bacterial virulence.

Elaboration of a benzofuran scaffold and evaluation of binding affinity and inhibition of Escherichia coli DsbA: A fragment-based drug design approach to novel antivirulence compounds.

Bacterial thiol-disulfide oxidoreductase DsbA is essential for bacterial virulence factor assembly and has been identified as a viable antivirulence target. Herein, we report a structure-based elaboration of a benzofuran hit that bound to the active site groove of Escherichia coli DsbA. Substituted phenyl groups were installed at the 5- and 6-position of the benzofuran using Suzuki-Miyaura coupling. HSQC NMR titration experiments showed dissociation constants of this series in the high µM to low mM range and X-ray crystallography produced three co-structures, showing binding in the hydrophobic groove, comparable with that of the previously reported benzofurans. The 6-(m-methoxy)phenyl analogue (2b), which showed a promising binding pose, was chosen for elaboration from the C-2 position. The 2,6-disubstituted analogues bound to the hydrophobic region of the binding groove and the C-2 groups extended into the more polar, previously un-probed, region of the binding groove. Biochemical analysis of the 2,6-disubsituted analogues showed they inhibited DsbA oxidation activity in vitro. The results indicate the potential to develop the elaborated benzofuran series into a novel class of antivirulence compounds.

Binding of a pyrimidine RNA base-mimic to SARS-CoV-2 nonstructural protein 9.

The coronaviral nonstructural protein 9 (Nsp9) is essential for viral replication; it is the primary substrate of Nsp12's pseudokinase domain within the viral replication transcription complex, an association that also recruits other components during different stages of RNA reproduction. In the unmodified state, Nsp9 forms an obligate homodimer via an essential GxxxG protein-interaction motif, but its ssRNA-binding mechanism remains unknown. Using structural biological techniques, here we show that a base-mimicking compound identified from a small molecule fragment screen engages Nsp9 via a tetrameric Pi-Pi stacking interaction that induces the formation of a parallel trimer-of-dimers. This oligomerization mechanism allows an interchange of "latching" N-termini, the charges of which contribute to a series of electropositive channels that suggests a potential interface for viral RNA. The identified pyrrolo-pyrimidine compound may also serve as a potential starting point for the development of compounds seeking to probe Nsp9's role within SARS-CoV-2 replication.

Association of asparagine concentration in wheat with cultivar, location, fertilizer, and their interaction.

The need to produce wheat with low asparagine concentration is of great importance as a measure to mitigate acrylamide concentration in wheat-based products. The association of asparagine concentration in Canadian bread wheat with cultivar, growing location, fertilizer and their interaction were investigated. Wheat cultivars (8) were grown in 2 locations under 4 fertilizer treatments in triplicate (which consisted of two nitrogen rates (90 or 120 lbs/acre) with or without 15 lbs sulphur per acre). The asparagine concentration ranged from 168.9 to 1050 µg/g and was significantly affected by cultivar, location, and their interaction but not fertilizer treatment. Location and cultivar were responsible for 80% and 14% of the variation, respectively. Some cultivars were not affected by location and maintained their low asparagine accumulation trait. Thus, breeding strategies should aim to identify cultivars that are low asparagine accumulating and are stable across different growing environments.

Characterization of the ergometric properties of commercial bioactive dairy peptides.

The thermodynamic properties of bioactive peptides provide insights into their functional behavior and their biological efficacy. We conducted precise analyses of the density, the ultrasonic velocity and the relative attenuation of serial dilutions of three commercial dairy peptides prepared by enzymatic methods. From these we determined the partial specific volume and the partial specific adiabatic compressibility coefficient for the peptides. At concentrations greater than ~2.5 â€‹mg â€‹mL-1, the apparent values for specific volume and adiabatic compressibility were constant, differing between the three peptides at ±3% for specific volume and ±70% for compressibility. Both specific volume and adiabatic compressibility were highly dependent on concentration, indicating the importance of precise low concentration measurements to obtain correct values for these thermodynamic parameters. From these parameters it was apparent that restructuring of water molecules around the peptides (and their associated counterions) led to compact solutes that were also incompressible. These thermodynamic analyses are critical for understanding how the properties and the beneficial effects of bioactive peptides are influenced by their chemical environment.

NMR fragment screening reveals a novel small molecule binding site near the catalytic surface of the disulfide-dithiol oxidoreductase enzyme DsbA from Burkholderia pseudomallei.

The presence of suitable cavities or pockets on protein structures is a general criterion for a therapeutic target protein to be classified as 'druggable'. Many disease-related proteins that function solely through protein-protein interactions lack such pockets, making development of inhibitors by traditional small-molecule structure-based design methods much more challenging. The 22 kDa bacterial thiol oxidoreductase enzyme, DsbA, from the gram-negative bacterium Burkholderia pseudomallei (BpsDsbA) is an example of one such target. The crystal structure of oxidized BpsDsbA lacks well-defined surface pockets. BpsDsbA is required for the correct folding of numerous virulence factors in B. pseudomallei, and genetic deletion of dsbA significantly attenuates B. pseudomallei virulence in murine infection models. Therefore, BpsDsbA is potentially an attractive drug target. Herein we report the identification of a small molecule binding site adjacent to the catalytic site of oxidized BpsDsbA. 1HN CPMG relaxation dispersion NMR measurements suggest that the binding site is formed transiently through protein dynamics. Using fragment-based screening, we identified a small molecule that binds at this site with an estimated affinity of KD ~ 500 µM. This fragment inhibits BpsDsbA enzymatic activity in vitro. The binding mode of this molecule has been characterized by NMR data-driven docking using HADDOCK. These data provide a starting point towards the design of more potent small molecule inhibitors of BpsDsbA.

Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiLX).

A bottleneck in fragment-based lead development is the lack of systematic approaches to elaborate the initial fragment hits, which usually bind with low affinity to their target. Herein, we describe an analysis using X-ray crystallography of a diverse library of compounds prepared using microscale parallel synthesis. This approach yielded an 8-fold increase in affinity and detailed structural information for the resulting complex, providing an efficient and broadly applicable approach to early fragment development.

Role of NaCl level on the handling and water mobility in dough prepared from four wheat cultivars.

In bread, NaCl plays a number of roles including improving flavor, functionality, dough handling, and prevention of sticky dough. Its reduction can create significant processing challenges. As such, the dough handling properties for four wheat cultivars (Pembina, Roblin, McKenzie, and Harvest) were investigated as a function of NaCl (0-4%) level. In terms of dough rheology, both cultivar and NaCl level were significant factors. The maximum deformation (Jmax ) in the dough decreased with increasing NaCl levels, indicating that the gluten network became stronger so that it was able to resist the imposed stress. For extensibility, increasing the levels of NaCl resulted in increased resistance to extension for all cultivars. Dough stickiness was shown to be both cultivar and salt level dependent, with weaker cultivars showing higher stickiness. Findings for water association indicated that with the addition of NaCl there was less free water among the different cultivars and an increase in the water associated with the starch-fraction. Dough morphology measurements supported rheology trends; the stronger dough producing cultivars created more elongated protein polymers with a unidirectional network whereas the weaker cultivars created porous multidirectional networks. Overall, Pembina and Roblin formed stronger gluten networks than McKenzie and Harvest, however, the effect of NaCl level was shown to be cultivar dependent. Findings indicate that careful cultivar selection will help mitigate challenges in dough handling within a reduced NaCl environment.

The effects of sodium reduction on the gas phase of bread doughs using synchrotron X-ray microtomography.

Globally, the bakery industry has a target of reducing sodium content in bread products. However, removing salt results in changes in the quality of bread through effects on dough's gas phase during the breadmaking process. Using synchrotron X-ray microtomography, the objective of this study was to investigate how sodium reduction induced changes in the gas phase parameters (i.e., gas volume fraction, bubble size distribution (BSD) and its time evolution) of non-yeasted doughs made from a wide range of formulations (i.e., wheat cultivar and water content) prepared with different mixing times. As salt content was reduced, a lower gas volume was retained in the dough by the end of mixing. Less gas bubbles were also retained if doughs were prepared from a stronger wheat cultivar, higher water content, and/or mixed for a shorter time. Rates of change in the median (R0) and the width (ε) of the fitted lognormal radius dependence of bubble volume fraction [BVF(R)] indicated that reduced sodium content permitted disproportionation to proceed more rapidly. Higher water content or longer mixing time also resulted in faster disproportionation, indicating that water content and mixing time can be manipulated as a means of increasing bubble stability against disproportionation during low-sodium breadmaking. An examination of relative changes in dough's gas phase parameters arising from sodium reduction demonstrated that wheat cultivar, water content and mixing time all affected dough's tolerance to sodium reduction. Therefore, attainment of good bread crumb cell structure in low-sodium bread formulas is a function of salt's effects on dough rheology in addition to its effect on yeast activity, so that dough formulation and mixing conditions also need to be considered.