Undesired Protein Research Articles

Synthesis and In Vitro Antileishmanial Efficacy of Novel Ethylene Glycol Analogues of Benzothiadiazine-1,1-dioxide.

Leishmaniasis is a vector-borne, parasitic disease affecting millions of people and animals worldwide. Current therapeutic options have proven to be ineffective in both treating the disease and preventing its spread. As a result, new drugs must be developed to effectively combat this disease. In this study, a series of 14 ethylene glycol analogues of benzothiadiazine-1,1-dioxide were synthesised to investigate their antileishmanial potential and cytotoxicity. Analogue 9, 2-(2-phenoxyethyl)-2H-benzo[e][1,2,4]thiadiazine-1,1-dioxide, was identified as the most inhibitory compound as it was observed to moderately inhibit the growth of L. major (IC50 103 μM) and L. donovani (IC50 153 μM) promastigotes. However, in general, the series presented with low biological activity, which may be attributed to reduced target affinity and/or undesired cell culture protein binding.

Co-stabilization effects of gluten/carrageenan to the over-heated myofibrillar protein: Inhibit the undesirable gel weakening and protein over-aggregations

High-temperature (120 °C) sterilization is an indispensable process for manufacturing ready-to-eat surimi products, yet risking the denaturation of their myofibrillar proteins (MP), thus significantly reducing the gelling properties. To resolve this problem, herein, a synergistic co-strengthening strategy was designed. The negatively charged polysaccharide carrageenan (CG) was introduced into MP simultaneously with wheat gluten, followed by 120 °C thermal treatment for 30 min. A substantial enhancement in mechanical strength, up to four times greater (from 9.86 to 42.38 g·cm), was observed for MP gels, which even surpassed that subjected to conventional gelation processes at 90 °C (36.53 g·cm). Gels that were concurrently added with gluten and CG exhibited porous networks, uniform water distribution, and improved water holding capacity. Accordingly, over-aggregation behaviors of MP were restricted, as evidenced by their reduced particle sizes and polymer dispersity index. Other heat-induced protein deteriorations at 120 °C, i.e., changes of secondary structures and disulfide bonding conformations, were also alleviated. By varying the CG types, it was shown that the κ-CG/gluten-added MP achieved highest gel strength, while the ι-CG/gluten combination may better stabilize the moisture in gel networks. This study introduces a co-reinforcement paradigm and scientific insights to the quality improvement of ready-to-eat meat products.

Overcoming Therapeutic Challenges of Antibiotic Delivery with Cubosome Lipid Nanocarriers.

Low discovery rates for new antibiotics, commercial disincentives to invest, and inappropriate use of existing drugs have created a perfect storm of antimicrobial resistance (AMR). This "silent pandemic" of AMR looms as an immense, global threat to human health. In tandem, many potential novel drug candidates are not progressed due to elevated hydrophobicity, which may result in poor intracellular internalization and undesirable serum protein binding. With a reducing arsenal of effective antibiotics, enabling technology platforms that improve the outcome of treatments, such as repurposing existing bioactive agents, is a prospective option. Nanocarrier (NC) mediated drug delivery is one avenue for amplifying the therapeutic outcome. Here, the performance of several antibiotic classes encapsulated within the lipid-based cubosomes is examined. The findings demonstrate that encapsulation affords significant improvements in drug concentration:inhibition outcomes and assists in other therapeutic challenges associated with internalization, enzyme degradation, and protein binding. We emphasize that a currently sidelined compound, novobiocin, became active and revealed a significant increase in inhibition against the pathogenic Gram-negative strain, Pseudomonas aeruginosa. Encapsulation affords co-delivery of multiple bioactives as a strategy for mitigating failure of monotherapies and tackling resistance. The rationale in optimized drug selection and nanocarrier choice is examined by transport modeling which agrees with experimental inhibition results. The results demonstrate that lipid nanocarrier encapsulation may alleviate a range of challenges faced by antibiotic therapies and increase the range of antibiotics available to treat bacterial infections.

Assessment of the Correlation Between Serum Phosphate Level and Muscle Strength as Measured by Handgrip Strength in Patients Treated With Hemodialysis.

Sarcopenia, commonly observed in patients treated with hemodialysis, correlates with low serum phosphate levels. Although normophosphatemia is desired, dietary phosphate restriction is difficult to achieve and may result in undesirable protein restriction. We aimed to evaluate whether hyperphosphatemia is associated with higher muscle strength in patients receiving hemodialysis treatment. A single-center prospective observational study. Ambulatory prevalent patients undergoing hemodialysis treatments in a dialysis unit of a tertiary hospital. Participants included prevalent patients treated with hemodialysis. All patients were above 18 years. Only patients with residual kidney function below 200 mL/24 hours were included to avoid bias. Muscle strength was measured by handgrip strength (HGS). Each patient repeated 3 measurements, and the highest value was recorded. Handgrip strength cutoffs for low muscle strength were defined as <27 kg in men and <16 kg in women. Biochemical parameters, including serum phosphate level, were driven from routine monthly blood tests. Hyperphosphatemia was defined as serum phosphate above 4.5 mg/dL. Handgrip strength results were compared to nutritional, anthropometric, and biochemical parameters-in particular phosphate level. Long-term mortality was recorded. Seventy-four patients were included in the final analysis. Handgrip strength was abnormally low in 33 patients (44.5%). Patients with abnormal HGS were older and more likely to have diabetes mellitus and lower albumin and creatinine levels. There was no correlation between HGS and phosphate level (r = 0.008, P = .945). On multivariable analysis, predictors of higher HGS were body mass index and creatinine. Diabetes mellitus and female sex predicted lower HGS. Hyperphosphatemia correlated with protein catabolic rate, blood urea nitrogen, and creatinine. On multivariable analysis, predictors of hyperphosphatemia were higher creatinine level, normal albumin level, and heart failure. During mean follow-up time of 7.66 ± 3.9 months, 11 patients died. Mortality was significantly higher in patients with abnormally low HGS compared with normal HGS (odds ratio = 9.32, P = .02). A single-center study. All measurements were performed at one time point without repeated assessments. Direct dietary intake, degree of physical activity, and medication compliance were not assessed. Hyperphosphatemia correlated with increased protein intake as assessed by protein catabolic rate in patients treated with hemodialysis; however, neither correlated with higher muscle strength as measured by HGS.Trial registration: MOH 202125213.

Investigation of the structure and morphology of modified materials based on polyvinyl chloride

The use of polyvinyl chloride in practice is associated with many difficulties due to the hydrophobic nature of the polymer surface. This can lead to great adverse consequences when used in technological processes of the chemical industry and hydrometallurgy. Due to its high hydrophobicity and low surface free energy, PVC has a low degree of wettability with water, resulting in low ion sorption capacity, as well as undesirable protein absorption and bacterial adhesion. The aim of the work was to increase the hydrophilicity of the surface of industrially produced powdered PVC by modifying it with various organic amines and, as a result, hydrophilic ion-exchange materials of various structures and morphology will be obtained on its basis. The course of the reactions was studied by potentiometric titration, IR spectroscopy, and diffractionometry. The correlation between the morphology and chemical properties of the products obtained in the studied reactions and the formation of new covalent bonds in the structure of the polymer matrix was investigated using IR spectroscopy and diffractionometry. The influence of the nature of the modifying reagent, solvent and temperature on the modification process has been established.

Undesirable protein sequence variations in maize genes that confer resistance to fungal pathogens and insect pests

Diseases and insect pests greatly impact sustainable production in maize. Maize inbred lines have varying levels of resistance to these pathogens and insects, but little is known about the diversity of their resistance proteins. In this study, genes encoding seven proteins that are involved in resistance to insects and pathogens in maize were analyzed in 46 maize inbred lines to elucidate the differences in amino acid sequences. The proteins of interest are superlectin, maizewin, hydrolase, geranyl geranyl transferase, quinone oxidoreductase, AIL1, and defensin. The protein sequences encoded by genes for superlectin, AIL1, and defensin were found to be disrupted in some maize inbreds but were conserved in others. The characterized disruptions resulted from single amino acid changes, insertions, or deletions. While the effect of single amino acid changes is hard to predict, insertions and deletions likely disrupt protein function, increasing the susceptibility of maize plants to insects and/or diseases. Functional resistance genes can be incorporated from the identified maize inbreds into commercial hybrids to promote enhanced insect and pathogen resistance.

Targeted kinase degradation via the KLHDC2 ubiquitin E3 ligase

Chemically induced protein degradation is a powerful strategy for perturbing cellular biochemistry. The predominant mechanism of action for protein degrader drugs involves an induced proximity between the cellular ubiquitin-conjugation machinery and a target. Unlike traditional small molecule enzyme inhibition, targeted protein degradation can clear an undesired protein from cells. We demonstrate here the use of peptide ligands for Kelch-like homology domain-containing protein 2 (KLHDC2), a substrate adapter protein and member of the cullin-2 (CUL2) ubiquitin ligase complex, for targeted protein degradation. Peptide-based bivalent compounds that can induce proximity between KLHDC2 and target proteins cause degradation of the targeted factors. The cellular activity of these compounds depends on KLHDC2 binding. This work demonstrates the utility of KLHDC2 for targeted protein degradation and exemplifies a strategy for the rational design of peptide-based ligands useful for this purpose.

Modification of Soft Wheat Protein for Improving Cake Quality by Superheated Steam Treatment of Wheat Grain.

Many varieties of soft wheat in China cannot fully satisfy the requirements of making high-quality cakes due to their undesirable protein properties, which leads to shortages of high-quality soft wheat flour. Therefore, a modification of soft wheat protein is essential for improving the quality of soft wheat and thus improving cake quality. In order to modify the protein properties of soft wheat used for cake production, superheated steam (SS) was used to treat soft wheat grains at 165 °C and 190 °C for 1, 2, 3, 4, and 5 min, respectively, followed by the milling of wheat grains to obtain refined wheat flour. The properties of proteins and cakes were analyzed using refined wheat flour as materials. First, changes in the structures of wheat proteins were analyzed by determining the solubility, molecular weight distribution and secondary structure of proteins in wheat flour. Secondly, changes in the functional properties of proteins were analyzed by determining the foaming properties and emulsifying properties of proteins in wheat flour. Finally, the specific volume and texture of cakes with wheat flour milled from SS-treated wheat were analyzed. At the initial stage of SS treatment, some of the gliadin and glutenin aggregated, and the gluten macro-polymer (GMP) contents increased. This allowed a more stable gluten network to form during dough kneading, leading to an improvement in dough elasticity. In addition, a short time period (1-3 min) of SS treatment improved the emulsifying properties and foaming ability of wheat protein, which helped to improve the specific volume and texture of cakes. Increasing the SS temperature from 165 °C to 190 °C reduced the optimal treatment time needed to improve cake quality from 3 min to 1 min. SS treatment for longer time (>3 min) periods led to severe protein aggregation and a decrease in the foaming ability and emulsifying properties of protein, which led to a deterioration in the cake quality. Thus, SS treatment at 165 °C for 1-3 min and 190 °C for 1 min could be a suitable method of improving the physicochemical properties of soft wheat used to make cakes with high specific volumes and good texture.

Radiotherapy-Triggered Proteolysis Targeting Chimera Prodrug Activation in Tumors.

Proteolysis targeting chimera (PROTAC) is an emerging protein degradation strategy, which shows excellent advantages in targeting those so-called "undruggable" proteins. However, the potential systemic toxicity of PROTACs caused by undesired off-tissue protein degradation may limit the application of PROTACs in clinical practice. Here we reported a radiotherapy-triggered PROTAC prodrug (RT-PROTAC) activation strategy to precisely and spatiotemporally control protein degradation through X-ray radiation. We demonstrated this concept by incorporating an X-ray inducible phenyl azide-cage to a bromodomain (BRD)-targeting PROTAC to form the first RT-PROTAC. The RT-PROTAC prodrug exhibits little activity but can be activated by X-ray radiation in vitro and in vivo. Activated RT-PROTAC degrades BRD4 and BRD2 with a comparable effect to the PROTAC degrader and shows a synergistic antitumor potency with radiotherapy in the MCF-7 xenograft model. Our work provides an alternative strategy to spatiotemporally control protein degradation in vivo and points to an avenue for reducing the undesired systemic toxicity of PROTACs.

Influence of clinical hemodialysis membrane morphology and chemistry on protein adsorption and inflammatory biomarkers released: In-situ synchrotron imaging, clinical and computational studies

Hemodialysis (HD) is often accompanied with activation of biochemical cascade reactions, caused by undesirable protein adsorption, which results in severe consequences for HD patients. Present research aims to study three hemodialysis membranes currently available in the Canadian hospitals of polyacrylonitrile (PAN), polyethersulfone (PES) and polyvinylidene fluoride (PVDF) and their interaction with three main human serum proteins: Human Serum Ablumin (HSA), Human Serum Fibrinogen (FB) and Human Serum Transferrin (TRF). In-situ synchrotron-based X-ray tomography (SR-μCT) was used to evaluate main membranes characteristics such as fiber diameter, pore size and their distribution, as well as to study the process of protein adsorption on the membranes surface and along membrane matrices. Scanning Electron Microscopy (SEM) was also used to investigate the morphology of proteins deposited on the membrane surface. Furthermore, interaction of membranes with inflammatory biomarkers was studied. Collected blood samples from HD patients were analyzed using Luminex assay for the inflammatory biomarkers of Serpin/Antitrombin-III, Properdin, C5a, 1L-1α, 1L-1β, IL-6 and TNF-α. Our results indicate the difference in the interaction of membranes with proteins is mainly attributed to a membrane surface charge and membrane chemistry. PAN and PES membranes, which are possessing high negative charge (-41.5mV and -68mV) and polar surface groups, would alter the morphology of adsorbed HAS and FB, while PVDF surface does not affect protein crystals growth. Furthermore, the molecular docking results showed that the highest interaction energy of human serum proteins was with PES membrane. The increased interaction of PES membrane with human serum proteins has triggered inflammation reactions. The release of C5a, IL-6 and Serpin cytokines for PES membrane was drastically higher compared to PAN and PVDF. The relative increase in those cytokine concentrations was 400-2000% for PES membrane, while it decreased by 10-40% for PAN and PVDF. It is worth noted that PVDF membrane had the lowest charge of -2.5 mV among investigated membranes, and it possessed the lowest interaction with human serum proteins and the least inflammation response.

Adsorption of Peptides onto Carbon Nanotubes Grafted with Poly(ethylene Oxide) Chains: A Molecular Dynamics Simulation Study.

Carbon nanotubes (CNTs) display exceptional properties that predispose them to wide use in technological or biomedical applications. To remove the toxicity of CNTs and to protect them against undesired protein adsorption, coverage of the CNT sidewall with poly(ethylene oxide) (PEO) is often considered. However, controversial results on the antifouling effectiveness of PEO layers have been reported so far. In this work, the interactions of pristine CNT and CNT covered with the PEO chains at different grafting densities with polyglycine, polyserine, and polyvaline are studied using molecular dynamics simulations in vacuum, water, and saline environments. The peptides are adsorbed on CNT in all investigated systems; however, the adsorption strength is reduced in aqueous environments. Save for one case, addition of NaCl at a physiological concentration to water does not appreciably influence the adsorption and structure of the peptides or the grafted PEO layer. It turns out that the flexibility of the peptide backbone allows the peptide to adopt more asymmetric conformations which may be inserted deeper into the grafted PEO layer. Water molecules disrupt the internal hydrogen bonds in the peptides, as well as the hydrogen bonds formed between the peptides and the PEO chains.

Dendrimer-siRNA Conjugates for Targeted Intracellular Delivery in Glioblastoma Animal Models.

Small interfering RNAs (siRNAs) are potent weapons for gene silencing, with an opportunity to correct defective genes and stop the production of undesirable proteins, with many applications in central nervous system (CNS) disorders. However, successful delivery of siRNAs to the brain parenchyma faces obstacles such as the blood-brain barrier (BBB), brain tissue penetration, and targeting of specific cells. In addition, siRNAs are unstable under physiological conditions and are susceptible to protein binding and enzymatic degradation, necessitating a higher dosage to remain effective. To address these issues and advance siRNA delivery, we report the development of covalently conjugated hydroxyl-terminated poly(amidoamine) (PAMAM) dendrimer-siRNA conjugates, demonstrated with a siRNA against GFP (siGFP) conjugate (D-siGFP) utilizing glutathione-sensitive linkers. This allows for precise nucleic acid loading, protects the payload from premature degradation, delivers the siRNA cargo into cells, and achieves significant GFP knockdown in vitro (∼40%) and in vivo (∼30%). Compared to commercially available delivery systems such as RNAi Max and Lipofectamine, D-siGFP retains the potency of the siRNA in vitro. In addition, the dendrimer-siGFP conjugate significantly enhances the half-life of siRNA in the presence of plasma and endonucleases and maintains the passive targeting ability of PAMAM dendrimers to reactive microglia. When administered intratumorally to orthotopic glioblastoma multiform tumors (GBM) in CX3CR-1GFP mice, D-siGFP localizes in tumor-associated macrophages (TAMs) within the tumor parenchyma, minimizing off-target effects in other cell populations. The facile conjugation strategy for dendrimer-siRNA conjugates presented here offers a promising approach for targeted, systemic intracellular delivery of siRNA, serving as a potential bridge for the clinical translation of RNAi therapies.

Developability Assessments of Monoclonal Antibody Candidates to Minimize Aggregation During Large-Scale Ultrafiltration and Diafiltration (UF-DF) Processing

Therapeutic proteins are subjected to a variety of stresses during manufacturing, storage or administration, that often lead to undesired protein aggregation and particle formation. Ultrafiltration-diafiltration (UF-DF) processing of monoclonal antibodies (mAbs) is one such manufacturing step that has been shown to result in such physical degradation. In this work, we explore the use of different analytical techniques and lab-scale setups as methodologies to predict and rank-order the aggregation potential of four different mAbs during large-scale UF-DF processing. In the first part of the study, a suite of biophysical techniques was applied to assess differences in their inherent bulk protein properties including conformational and colloidal stability in a PBS buffer. Additionally, the inherent interfacial properties of these mAbs in PBS were measured using a Langmuir trough technique. In the next part of the study, several different scale-down lab models were evaluated including a lab bench-scale UF-DF setup, mechanical stress (shaking/stirring) studies in vials, and application of interfacial dilatational stress using a Langmuir trough to assess protein particle formation in different UF-DF processing buffers. Taken together, our results demonstrate the ability of a Langmuir-trough methodology to accurately predict the mAb instability profile observed during large scale UF-DF processing.

Zwitterionic Modification of Polyethyleneimine for Efficient In Vitro siRNA Delivery.

Polyethylenimine (PEI) has been widely used in gene delivery. However, its high cytotoxicity and undesired non-specific protein adsorption hinder the overall delivery efficacy and the practical applications of PEI-based gene delivery systems. In this study, we prepared hydrophobically modified PEIs (H-PEIs) via the reaction of octanal with 40% of primary amines in PEI25k and PEI10k, respectively. Two common zwitterionic molecules, 1,3-propanesultone and β-propiolactone, were then used for the modification of the resulting H-PEIs to construct polycationic gene carriers with zwitterionic properties (H-zPEIs). The siRNA delivery efficiency and cytotoxicity of these materials were evaluated in Hela-Luc and A549-Luc cell lines. Compared with their respective parental H-PEIs, different degrees of zwitterionic modification showed different effects in reducing cytotoxicity and delivery efficiency. All zwitterion-modified PEIs showed excellent siRNA binding capacity, reduced nonspecific protein adsorption, and enhanced stability upon nuclease degradation. It is concluded that zwitterionic molecular modification is an effective method to construct efficient vectors by preventing undesired interactions between polycationic carriers and biomacromolecules. It may offer insights into the modification of other cationic carriers of nucleic acid drugs.

The competing influence of surface roughness, hydrophobicity, and electrostatics on protein dynamics on a self-assembled monolayer.

Surface morphology, in addition to hydrophobic and electrostatic effects, can alter how proteins interact with solid surfaces. Understanding the heterogeneous dynamics of protein adsorption on surfaces with varying roughness is experimentally challenging. In this work, we use single-molecule fluorescence microscopy to study the adsorption of α-lactalbumin protein on the glass substrate covered with a self-assembled monolayer (SAM) with varying surface concentrations. Two distinct interaction mechanisms are observed: localized adsorption/desorption and continuous-time random walk (CTRW). We investigate the origin of these two populations by simultaneous single-molecule imaging of substrates with both bare glass and SAM-covered regions. SAM-covered areas of substrates are found to promote CTRW, whereas glass surfaces promote localized motion. Contact angle measurements and atomic force microscopy imaging show that increasing SAM concentration results in both increasing hydrophobicity and surface roughness. These properties lead to two opposing effects: increasing hydrophobicity promotes longer protein flights, but increasing surface roughness suppresses protein dynamics resulting in shorter residence times. Our studies suggest that controlling hydrophobicity and roughness, in addition to electrostatics, as independent parameters could provide a means to tune desirable or undesirable protein interactions with surfaces.

PROTACs: A Hope for Breast Cancer Patients?

Breast Cancer (BC) is the most widely occurring disease in women. A massive number of women are diagnosed with breast cancer, and many lose their lives every year. Cancer is the leading cause of death worldwide, posing a formidable challenge to the current medication difficulties. The main objective of this study is to examine and explore novel therapy (PROTAC) and its effectiveness against breast cancer. The literature search was conducted across Medline, Cochrane, ScienceDirect, Wiley Online, Google Scholar, PubMed, and Bentham Sciences from 2001 to 2020. The articles collected were screened, segregated, and selected papers were included for writing the review article. A novel innovation emerged around two decades ago that has great potential to overcome the limitations and provide future direction for the treatment of many diseases, which has presently not many therapeutic options available and are regarded as incurable with traditional techniques. That innovation is called PROTAC (Proteolysis Targeting Chimera), which can efficaciously ubiquitinate and debase cancer, encouraging proteins through noncovalent interaction. PROTACs constituted of two active regions isolated by a linker are equipped for eliminating explicit undesirable protein. It is empowering greater sensitivity to "drugresistant targets" and a more prominent opportunity to influence non-enzymatic function. PROTACs have been demonstrated to show better target selectivity contrasted with traditional small-molecule inhibitors. So far, the most investigation into PROTACs mainly concentrated on cancer treatment applications, including breast cancer. The treatment of different ailments may benefit the patients from this blossoming innovation.

Nickel (II) and Cobalt (II) Alginate Biopolymers as a "Carry and Release" Platform for Polyhistidine-Tagged Proteins.

Protein immobilization using biopolymer scaffolds generally involves undesired protein loss of function due to denaturation, steric hindrance or improper orientation. Moreover, most methods for protein immobilization require expensive reagents and laborious procedures. This work presents the synthesis and proof of concept application of two alginate hydrogels that are able to bind proteins with polyhistidine tags by means of interaction with the crosslinking cations. Nickel (II) and cobalt (II) alginate hydrogels were prepared using a simple ionic gelation method. Hydrogels were characterized by optical microscopy and AFM, and evaluated for potential cytotoxicity. In addition, binding capacity was tested towards proteins with or without HisTAG. Hydrogels had moderate cytotoxicity and were able to exclusively bind polyhistidine-tagged proteins with a binding capacity of approximately 300 µg EGFP (enhanced green fluorescent protein) per 1 mL of hydrogel. A lyophilized hydrogel-protein complex dissolved upon the addition of PBS and allowed the protein release and regain of biological activity. In conclusion, the nickel (II) and cobalt (II) alginate biopolymers provided an excellent platform for the “carry and release” of polyhistidine-tagged proteins.

Malting and Wort Production Potential of the Novel Grain Kernza (Thinopyrum intermedium)

As the environmental impacts of beer are of increasing concern to maltsters, brewers, and consumers, perennial cereal crops can offer a more sustainable solution. One new cereal species of interest to the brewing industry is intermediate wheatgrass (Thinopyrum intermedium subsp. intermedium), developed by The Land Institute, in Salina, Kansas, U.S.A., under the branded name Kernza®. It has been touted as a more sustainable alternative to barley and wheat in its requirements for less water and nutrient additions and reduced tilling of agricultural fields. To date, no published research has been performed to assess the potential for this grain for the malt and beer industries as a barley replacement. Here, the “M5” variety Kernza grain was micromalted and the finished malt was compared with both the raw grain and to a reference raw and malted barley (Hordeum vulgare L. var. Copeland). All samples were analyzed for starch gelatinization temperatures via differential scanning calorimetry, amino acid composition, alpha-amylase, diastatic power (DP), total and soluble nitrogen and protein, Kolbach Index (KI), extract, wort free alpha-amino nitrogen (FAN), wort β-glucan, wort color, pH, and clarity. The Kernza malt produced sufficient extract and FAN for typical fermentations with low β-glucan content. However, extract and FAN in the Kernza malts were lower than in the barley reference, and the Kernza worts exhibited higher levels of undesirable soluble protein and haze. Interestingly, the DP for both the raw and malted Kernza were similarly high, indicating that both of the raw grains exhibit high enzymatic activity, which malting did not increase substantially. Results support that Kernza could be an acceptable candidate for malting and subsequent wort production; however, specific techniques may be required to utilize this malt most effectively. Supplemental data for this article is available online at https://doi.org/10.1080/03610470.2022.2026662 .

Whole proteome mapping of compound-protein interactions.

Off-target binding is one of the primary causes of toxic side effects of drugs in clinical development, resulting in failures of clinical trials. While off-target drug binding is a known phenomenon, experimental identification of the undesired protein binders can be prohibitively expensive due to the large pool of possible biological targets. Here, we propose a new strategy combining chemical similarity principle and deep learning to enable proteome-wide mapping of compound-protein interactions. We have developed a pipeline to identify the targets of bioactive molecules by matching them with chemically similar annotated "bait" compounds and ranking them with deep learning. We have constructed a user-friendly web server for drug-target identification based on chemical similarity (DRIFT) to perform searches across annotated bioactive compound datasets, thus enabling high-throughput, multi-ligand target identification, as well as chemical fragmentation of target-binding moieties.

Targeted Degradation of Proteins — The Ubiquitin System

Proteins are the engines of all forms of life, for humans and for all the plant and animal kingdoms. Proteins are used both to build organs (such as bones, muscles, and skin) and to perform bodily functions. These functions range from digestion (processing food and converting it into energy), to enabling movement and sensation (sight and hearing), to protecting the body from foreign invaders with our antibodies, which are also proteins. What are proteins? They can be compared to words in a language that contains letters. In the Hebrew alphabet, there are 26 letters out of which countless words can be composed. But when we write, we use just a fraction of these infinite options, with the average number of letters in a word ranging between 3 and 8. The biological “protein alphabet” is comprised of 20 “letters” called amino acids, which are the building blocks of the proteins that make up the body. Proteins are chains of amino acid, linked together in a specific order governed by the DNA. Unlike the words of a spoken language, the average protein consists of hundreds of amino acids. The extensive length of proteins and the chemical composition of the amino acids make proteins sensitive to many factors, such as high temperatures, radiation, and chemicals. All these factors damage proteins and alter their fragile structures, negatively affecting how they function. When proteins are damaged or when they finish performing their functions and are no longer needed, the body breaks them down. With my doctoral adviser, Prof. Avram Hershko, and our research collaborator, Prof. Irwin Rose from the Fox Chase Cancer Center in Philadelphia, we discovered the mechanism responsible for targeted degradation of proteins in cells. This degradation can recognize damaged proteins or proteins that are not needed anymore, while leaving intact the “healthy,” functional ones. This mechanism is called the ubiquitin system after its principal protein, ubiquitin, which was the first protein we discovered in the system. Ubiquitin’s role is to tag undesirable proteins so that the cell’s “grinder” can recognize them and break them down, enabling the cell to function normally. In this article, we will explain the story of proteins and the ubiquitin system that we discovered in a study that earned us, among other prizes, the Nobel Prize in Chemistry in 2004.