Osteoprotegerin a jeho ligand (tzv. RANKL) jsou působky, které ovlivňují významným způsobem kostní resorpci (OPG inhibuje osteoklastogenezi a jeho ligand ji stimuluje). Obě látky jsou produkovány osteoblastickou buněčnou linií, vyskytují se v oběhu ve volné formě, a lze je tudíž měřit. Účinky OPG/RANKL jsou v posledních letech intenzívně studovány. Na animálních modelech bylo prokázáno, že OPG deficitní myši mají osteoporózu a naopak, myši s defektním genem pro ligand OPG mají osteopetrózu. Také podle výsledků většiny klinických studií se zdá, že existuje negativní souvislost mezi OPG a kostní denzitou. Existují pokusy o uplatnění modelu OPG/RANKL při výzkumu maligních primárních i sekundárních kostních ložisek, myelomu, cévních kalcifikací atp. Terapeutické podávání osteoprotegerinu v experimentu se osvědčilo u jedinců s těžkou osteoporózou, destruktivními chorobami skeletu, u metastazujících karcinomů mamy, tlustého střeva a prostaty, osteosarkomu či po ovarektomii. U takto léčených jedinců došlo také k významné redukci experimentálně navozených cévních kalcifikací.
Osteoprotegerin and its ligand (so-called RANKL) are substances which influence in an important way bone resorption (OPG inhibits osteoclastogenesis and its ligand stimulates it). Both substances are produced by the osteoblastic cell line, they are found in the blond stream in the free form and they can thus be estimated. The effects of OPG/RANKL are intensely studied in retem years. On animal models evidence was provided tkat OPG deficient mice have osteoporosis and vice ýersa. Also according to the results of the majority of clinical studies it seems tkat there exists an invers relationship between OPG and bone density. There are attempts to apply the OPG/RANKL method in research of malignant primary and secondary osseous fotí, myelomas, vascular calcifications etc. Therapeutic administration of osteoprotegerin in experiments proved useful in individuals with severe osteoporosis, destructive skeletal disease, in metastatizing carcinomas of the mammary gland, large intestine and prostaty, osteosarcoma or after ovariectomy. In thus treated subjects also a significant reduction of experimentally induced calcifications occurred.
- MeSH
- Osteopetrosis etiology drug therapy MeSH
- Cytokines physiology therapeutic use MeSH
- Humans MeSH
- Multiple Myeloma etiology drug therapy MeSH
- Disease Models, Animal MeSH
- NF-kappa B physiology therapeutic use MeSH
- Osteoporosis etiology drug therapy MeSH
- Bone Resorption MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Review MeSH
- Comparative Study MeSH
The new version of the TRITON program provides user-friendly graphical tools for modeling protein mutants using the external program MODELLER and for docking ligands into the mutants using the external program AutoDock. TRITON can now be used to design ligand-binding proteins, to study protein-ligand binding mechanisms or simply to dock any ligand to a protein. Availability: Executable files of TRITON are available free of charge for academic users at http://ncbr.chemi.muni.cz/triton/
- MeSH
- Algorithms MeSH
- Models, Chemical MeSH
- Financing, Organized MeSH
- Ligands MeSH
- Models, Molecular MeSH
- Computer Graphics MeSH
- Computer Simulation MeSH
- Protein Engineering methods MeSH
- Proteins chemistry ultrastructure MeSH
- Drug Design MeSH
- Software MeSH
- User-Computer Interface MeSH
- Protein Binding MeSH
- Binding Sites MeSH
BACKGROUND: Bark beetles are major pests of conifer forests, and their behavior is primarily mediated via olfaction. Targeting the odorant receptors (ORs) may thus provide avenues towards improved pest control. Such an approach requires information on the function of ORs and their interactions with ligands, which is also essential for understanding the functional evolution of these receptors. Hence, we aimed to identify a high-quality complement of ORs from the destructive spruce bark beetle Ips typographus (Coleoptera, Curculionidae, Scolytinae) and analyze their antennal expression and phylogenetic relationships with ORs from other beetles. Using 68 biologically relevant test compounds, we next aimed to functionally characterize ecologically important ORs, using two systems for heterologous expression. Our final aim was to gain insight into the ligand-OR interaction of the functionally characterized ORs, using a combination of computational and experimental methods. RESULTS: We annotated 73 ORs from an antennal transcriptome of I. typographus and report the functional characterization of two ORs (ItypOR46 and ItypOR49), which are responsive to single enantiomers of the common bark beetle pheromone compounds ipsenol and ipsdienol, respectively. Their responses and antennal expression correlate with the specificities, localizations, and/or abundances of olfactory sensory neurons detecting these enantiomers. We use homology modeling and molecular docking to predict their binding sites. Our models reveal a likely binding cleft lined with residues that previously have been shown to affect the responses of insect ORs. Within this cleft, the active ligands are predicted to specifically interact with residues Tyr84 and Thr205 in ItypOR46. The suggested importance of these residues in the activation by ipsenol is experimentally supported through site-directed mutagenesis and functional testing, and hydrogen bonding appears key in pheromone binding. CONCLUSIONS: The emerging insight into ligand binding in the two characterized ItypORs has a general importance for our understanding of the molecular and functional evolution of the insect OR gene family. Due to the ecological importance of the characterized receptors and widespread use of ipsenol and ipsdienol in bark beetle chemical communication, these ORs should be evaluated for their potential use in pest control and biosensors to detect bark beetle infestations.
2nd ed. 458 s.
- MeSH
- Biochemistry MeSH
- Ligands MeSH
- Radioligand Assay MeSH
- Receptors, Drug physiology MeSH
- Structure-Activity Relationship MeSH
- Publication type
- Monograph MeSH
- Conspectus
- Biochemie. Molekulární biologie. Biofyzika
- NML Fields
- biochemie
Several small-molecule ligands specifically bind and stabilize G-quadruplex (G4) nucleic acid structures, which are considered to be promising therapeutic targets. G4s are polymorphic structures of varying stability, and their formation is dynamic. Here, we investigate the mechanisms of ligand binding to dynamically populated human telomere G4 DNA by using the bisquinolinium based ligand Phen-DC3 and a combination of single-molecule FRET microscopy, ensemble FRET and CD spectroscopies. Different cations are used to tune G4 polymorphism and folding dynamics. We find that ligand binding occurs to pre-folded G4 structures and that Phen-DC3 also induces G4 formation in unfolded single strands. Following ligand binding to dynamically populated G4s, the DNA undergoes pronounced conformational redistributions that do not involve direct ligand-induced G4 conformational interconversion. On the contrary, the redistribution is driven by ligand-induced G4 folding and trapping of dynamically populated short-lived conformation states. Thus, ligand-induced stabilization does not necessarily require the initial presence of stably folded G4s.
- MeSH
- Quinolines chemistry metabolism MeSH
- G-Quadruplexes * MeSH
- Nucleic Acid Conformation MeSH
- Humans MeSH
- Ligands * MeSH
- Fluorescence Resonance Energy Transfer MeSH
- Molecular Dynamics Simulation MeSH
- Telomere chemistry MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Accurate estimation of protein-ligand binding affinity is the cornerstone of computer-aided drug design. We present a universal physics-based scoring function, named SQM2.20, addressing key terms of binding free energy using semiempirical quantum-mechanical computational methods. SQM2.20 incorporates the latest methodological advances while remaining computationally efficient even for systems with thousands of atoms. To validate it rigorously, we have compiled and made available the PL-REX benchmark dataset consisting of high-resolution crystal structures and reliable experimental affinities for ten diverse protein targets. Comparative assessments demonstrate that SQM2.20 outperforms other scoring methods and reaches a level of accuracy similar to much more expensive DFT calculations. In the PL-REX dataset, it achieves excellent correlation with experimental data (average R2 = 0.69) and exhibits consistent performance across all targets. In contrast to DFT, SQM2.20 provides affinity predictions in minutes, making it suitable for practical applications in hit identification or lead optimization.
- MeSH
- Ligands MeSH
- Proteins * metabolism MeSH
- Drug Design * MeSH
- Thermodynamics MeSH
- Protein Binding MeSH
- Publication type
- Journal Article MeSH
PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively.
- MeSH
- Benchmarking MeSH
- Datasets as Topic MeSH
- Protein Interaction Domains and Motifs MeSH
- Internet MeSH
- Protein Conformation, alpha-Helical MeSH
- Protein Conformation, beta-Strand MeSH
- Humans MeSH
- Ligands MeSH
- Proteins chemistry metabolism MeSH
- Amino Acid Sequence MeSH
- Software * MeSH
- Machine Learning * MeSH
- Thermodynamics MeSH
- Protein Binding MeSH
- Binding Sites MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
G-rich aptamers such as AS1411 are small oligonucleotides that present several benefits comparatively to monoclonal antibodies, since they are easier to manufacture and store, have small size and do not stimulate an immune response. We analyzed AT11-B1, a modified sequence of AT11 (itself a modified version of AS1411), in which one thymine was removed from the bulge region. We studied G-quadruplex (G4) formation/stabilization using PhenDC3, PDS, BRACO-19, TMPyP4 and 360A ligands by different biophysical techniques, namely circular dichroism (CD), Förster resonance energy transfer (FRET-melting) and nuclear magnetic resonance (NMR). The CD spectra showed that AT11-B1 adopts a predominant G4 of parallel topology when the buffer contains KCl or when ligands are added. PhenDC3 induced a ΔTm of 30 °C or more of the G4 structure as shown by CD- and FRET-melting experiments. The ligands demonstrate high affinity for AT11-B1 G4 and the NMR studies revealed that the AT11-B1 G4 involves four G-tetrad layers. The in silico studies suggest that all ligands bind AT11-B1 G4, namely, by stacking interactions, with the possible exception of PDS that may bind to the loop/groove interface. In addition, molecular dynamics simulations revealed that nucleolin (NCL) interacts with the AT11-B1 G4 structure through the RNA binding domain (RBD) 2 and the 12-residue linker between RBD1,2. Moreover, AT11-B1 G4 was internalized into a NCL-positive tongue squamous cell carcinoma cell line. In a nutshell, this study may help the identification of the ligands scaffolds to bind and stabilize AT11-B1, improving the targeting towards NCL that is overexpressed in cancer cells.
- MeSH
- Aptamers, Nucleotide * chemistry MeSH
- G-Quadruplexes * MeSH
- Humans MeSH
- Ligands MeSH
- Tongue Neoplasms * MeSH
- Carcinoma, Squamous Cell * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
