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Expert Reviews in Molecular Medicine Apr 2024Target deconvolution can help understand how compounds exert therapeutic effects and can accelerate drug discovery by helping optimise safety and efficacy, revealing... (Review)
Review
Target deconvolution can help understand how compounds exert therapeutic effects and can accelerate drug discovery by helping optimise safety and efficacy, revealing mechanisms of action, anticipate off-target effects and identifying opportunities for therapeutic expansion. Chemoproteomics, a combination of chemical biology with mass spectrometry has transformed target deconvolution. This review discusses modification-free chemoproteomic approaches that leverage the change in protein thermodynamics induced by small molecule ligand binding. Unlike modification-based methods relying on enriching specific protein targets, these approaches offer proteome-wide evaluations, driven by advancements in mass spectrometry sensitivity, increasing proteome coverage and quantitation methods. Advances in methods based on denaturation/precipitation by thermal or chemical denaturation, or by protease degradation are evaluated, emphasising the evolving landscape of chemoproteomics and its potential impact on future drug-development strategies.
Topics: Humans; Proteome; Drug Discovery; Mass Spectrometry; Drug Development
PubMed: 38604802
DOI: 10.1017/erm.2024.6 -
Nature Communications Nov 2023The dense stroma of desmoplastic tumor limits nanotherapeutic penetration and hampers the antitumor immune response. Here, we report a denaturation-and-penetration...
The dense stroma of desmoplastic tumor limits nanotherapeutic penetration and hampers the antitumor immune response. Here, we report a denaturation-and-penetration strategy and the use of tin monosulfide nanoparticles (SnSNPs) as nano-sonosensitizers that can overcome the stromal barrier for the management of desmoplastic triple-negative breast cancer (TNBC). SnSNPs possess a narrow bandgap (1.18 eV), allowing for efficient electron (e)-hole (h) pair separation to generate reactive oxygen species under US activation. More importantly, SnSNPs display mild photothermal properties that can in situ denature tumor collagen and facilitate deep penetration into the tumor mass upon near-infrared irradiation. This approach significantly enhances sonodynamic therapy (SDT) by SnSNPs and boosts antitumor immunity. In mouse models of malignant TNBC and hepatocellular carcinoma (HCC), the combination of robust SDT and enhanced cytotoxic T lymphocyte infiltration achieves remarkable anti-tumor efficacy. This study presents an innovative approach to enhance SDT and antitumor immunity using the denaturation-and-penetration strategy, offering a potential combined sono-immunotherapy approach for the cancer nanomedicine field.
Topics: Humans; Animals; Mice; Ultrasonic Therapy; Carcinoma, Hepatocellular; Triple Negative Breast Neoplasms; Liver Neoplasms; Neoplasms; Reactive Oxygen Species; Nanoparticles; Cell Line, Tumor
PubMed: 37914681
DOI: 10.1038/s41467-023-42509-7 -
Extremophiles : Life Under Extreme... Nov 2023Lignocellulolytic enzymes are used in different industrial and environmental processes. The rigorous operating circumstances of these industries, however, might prevent... (Review)
Review
Lignocellulolytic enzymes are used in different industrial and environmental processes. The rigorous operating circumstances of these industries, however, might prevent these enzymes from performing as intended. On the other side, extremozymes are enzymes produced by extremophiles that can function in extremely acidic or basic; hot or cold; under high or low salinity conditions. These severe conditions might denature the normal enzymes that are produced by mesophilic microorganisms. The increased stability of these enzymes has been contributed to a number of conformational modifications in their structures. These modifications may result from a few amino acid substitutions, an improved hydrophobic core, the existence of extra ion pairs and salt bridges, an increase in compactness, or an increase in positively charged amino acids. These enzymes are the best option for industrial and bioremediation activities that must be carried out under difficult conditions due to their improved stability. The review, therefore, discusses lignocellulolytic extremozymes, their structure and mechanisms along with industrial and biotechnological applications.
Topics: Extremophiles; Biotechnology; Acids; Amino Acids
PubMed: 37950773
DOI: 10.1007/s00792-023-01314-2 -
Langmuir : the ACS Journal of Surfaces... Oct 2023DNA nanotechnology offers an unrivaled programmability of plasmonic nanoassemblies based on encodable Watson-Crick basepairing. However, it is very challenging to build...
DNA nanotechnology offers an unrivaled programmability of plasmonic nanoassemblies based on encodable Watson-Crick basepairing. However, it is very challenging to build rigidified three-dimensional supracolloidal assemblies with strong electromagnetic coupling and a self-confined exterior shape. We herein report an alternative strategy based on a DNA condensation reaction to make such structures. Using DNA-grafted gold nanoparticles as building blocks and metal ions with suitable phosphate affinities as abiological DNA-bonding agents, a seedless growth of spheroidal supraparticles is realized via metal-ion-induced DNA condensation. Some governing rules are disclosed in this process, including kinetic and thermodynamic effects stemming from electrostatic and coordinative forces with different interaction ranges. The supraballs are tailorable by adjusting the volumetric ratio between DNA grafts and gold cores and by overgrowing extra gold layers toward tunable plasmon coupling. Various appealing and highly desirable properties are achieved for the resulting metaballs, including (i) chemical reversibility and fixation ability, (ii) stability against denaturant, salt, and molecular adsorbates, (iii) enriched and continuously tunable plasmonic hotspots, (iv) permeability to small guest molecules and antifoulingness against protein contaminates, and (v) Raman-enhancing and photocatalytic activities. Innovative applications are thus foreseeable for this emerging class of meta-assemblies in contrast to what is achieved by DNA-basepaired ones.
Topics: Gold; Surface Plasmon Resonance; Metal Nanoparticles; DNA; Nanotechnology
PubMed: 37725679
DOI: 10.1021/acs.langmuir.3c01860 -
International Journal of Molecular... Feb 2024Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their... (Review)
Review
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
Topics: Protein Stability; Proteins; Amino Acids; Fluorometry; Biological Assay; Protein Denaturation
PubMed: 38339045
DOI: 10.3390/ijms25031764 -
Chembiochem : a European Journal of... Aug 2023This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this... (Review)
Review
This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.
Topics: Protein Denaturation; Proteins; Magnetic Resonance Spectroscopy; Protein Unfolding; Protein Conformation; Thermodynamics; Protein Folding; Cold Temperature
PubMed: 37154795
DOI: 10.1002/cbic.202300164 -
Ageing Research Reviews Nov 2023Osteoarthritis (OA) is a degenerative joint disease, affecting 32.5 million US adults or 242 million people worldwide. There is no cure for OA. Many animal and clinical... (Review)
Review
Osteoarthritis (OA) is a degenerative joint disease, affecting 32.5 million US adults or 242 million people worldwide. There is no cure for OA. Many animal and clinical trials showed that oral administration of undenatured type II collagen could significantly reduce the incidence of OA or alleviate the symptoms of articular cartilage. Type II collagen is an important component of cartilage matrix. This article reviewed research progress of undenatured type II collagen including its methods of extraction and preparation, structure and characterization, solubility, thermal stability, gastrointestinal digestive stability, its role in improving OA, and the mechanism of its action in improving OA. Type II collagen has been extensively explored for its potential in improving arthritis. Methods of extraction of type II collagen are inefficient and tedious. The method of limited enzymatic hydrolysis is mainly used to prepare soluble undenatured type II collagen (SC II). The solubility, thermal and gastrointestinal digestive stability of SC II are affected by the sources of raw material, pH, salt ions, and temperature. Oral administration of undenatured type II collagen improves OA, whereas its activity is affected by the sources, degree of denaturalization, intervention methods and doses. However, the influence of the structure of undenatured type II collagen on its activity and the mechanism are unclear. The findings in this review support that undenatured type II collagen can be used in the intervention or auxiliary intervention of patients with OA.
Topics: Animals; Humans; Collagen Type II; Cartilage, Articular; Osteoarthritis
PubMed: 37774932
DOI: 10.1016/j.arr.2023.102080 -
Biotechnology Journal Jan 2024Laccases have shown to be efficient biocatalysts for the removal of recalcitrant pollutants from wastewater. Thus, they catalyze the oxidation of a wide variety of... (Review)
Review
Laccases have shown to be efficient biocatalysts for the removal of recalcitrant pollutants from wastewater. Thus, they catalyze the oxidation of a wide variety of organic compounds by reducing molecular oxygen to water. However, the use of free laccases holds several drawbacks such as poor reusability, high cost, low stability and sensitivity to different denaturing agents that may occur in wastewater. Such drawbacks can be circumvented by immobilizing laccase enzymes in/on solid carriers. Hence, during the last decades different approaches considering various techniques and solid carriers to immobilize laccase enzymes have been developed and tested for the removal of pollutants from wastewater. To scale up wastewater treatment bioprocesses, immobilized laccases are placed in different reactor configurations.
Topics: Enzymes, Immobilized; Wastewater; Laccase; Bioreactors; Water Purification; Environmental Pollutants
PubMed: 37750809
DOI: 10.1002/biot.202300354 -
Chembiochem : a European Journal of... Apr 2024The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble... (Review)
Review
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
Topics: Protein Conformation, beta-Strand; Peptides; Proteins; Protein Folding; Temperature
PubMed: 38275210
DOI: 10.1002/cbic.202300745 -
Genes Mar 2024The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The... (Review)
Review
The polymerase chain reaction (PCR) has played a fundamental role in our understanding of the world, and has applications across a broad range of disciplines. The introduction of PCR into forensic science marked the beginning of a new era of DNA profiling. This era has pushed PCR to its limits and allowed genetic data to be generated from trace DNA. Trace samples contain very small amounts of degraded DNA associated with inhibitory compounds and ions. Despite significant development in the PCR process since it was first introduced, the challenges of profiling inhibited and degraded samples remain. This review examines the evolution of the PCR from its inception in the 1980s, through to its current application in forensic science. The driving factors behind PCR evolution for DNA profiling are discussed along with a critical comparison of cycling conditions used in commercial PCR kits. Newer PCR methods that are currently used in forensic practice and beyond are examined, and possible future directions of PCR for DNA profiling are evaluated.
Topics: Humans; Polymerase Chain Reaction; Forensic Sciences; DNA Fingerprinting; DNA; Forensic Genetics
PubMed: 38674373
DOI: 10.3390/genes15040438