Compounds that bind. Medical search. Frequent questions

We adopted a distinct approach aimed initially at interfering with protein-protein interactions of RAS, and other so-called undruggable targets like transcription factors, using molecular biology tools called intracellular antibodies that bind to target proteins inside cells. (cancer.gov)
proposed an end-to-end learning method to predict the activity of compounds for novel target proteins. (biomedcentral.com)
Recent studies have shown a high prevalence of S100 proteins in PDAC, in particular the calcium-binding protein S100P. (brighton.ac.uk)
Identifying persistent organic pollutants bound to intact proteins: endocrine-disrupting industrial compounds. (birmingham.ac.uk)
RNA binding proteins co-localize with small tau inclusions in tauopathy. (nih.gov)

Aptamers are engineered molecules that can bind to specific target compounds with high affinity and selectivity, making them valuable tools in various applications. (neoaptamers.com)
Extensive efforts have been made to improve the affinity and selectivity of these compounds and the continuous expansion of related research makes this chemistry even more promising. (edu.sa)

Here we use a Capture Compound with S -adenosyl- L -homocysteine-binding as selectivity function to isolate methyltransferases from an Escherichia coli whole cell lysate and identify them by MS. (jove.com)
However, aptamers can still exhibit high selectivity, allowing them to differentiate between closely related compounds. (neoaptamers.com)
Specificity goes beyond selectivity by necessitating that the aptamer exclusively binds to a single compound without any cross-reactivity with other molecules. (neoaptamers.com)
Attaining absolute specificity can be demanding, as it requires an aptamer to exhibit both a high degree of selectivity and pinpoint accuracy in its binding. (neoaptamers.com)
Our team of dedicated scientists employs cutting-edge technologies and innovative methodologies to meticulously characterize the unique binding sites on target molecules, ensuring that the developed aptamers exhibit exceptional selectivity and accuracy. (neoaptamers.com)
The set of composite films has shown high selectivity to the analyzed volatile compounds. (us-csic.es)

root phenolic compounds by ring nematodes, Mesocriconema xenoplax. (usda.gov)

It predicts the binding energy of a compound to a target protein by virtually docking the compound (i.e., ligand) with a binding site (i.e., pocket) of a target protein surface. (biomedcentral.com)
We find evidence for the selective allosteric activation and inhibition of Hsp90's conformational transition toward the closed state in response to ligand binding and shed valuable insight to further the understanding of allosteric drug design and Hsp90's complex allosteric mechanism of action. (nature.com)
High resolution crystal structure of Adenosine A2 receptor (AA2AR) in complex with agonist UK-432097 makes possible rational design of small molecules specifically targeting C5' substitutions of the agonist ribose ring, making possible more high affinity and subtype selective binding and potentially ligand specific modulation of adenosine receptor function. (nih.gov)
High resolution crystal structure makes possible rational design of small molecules specifically targeting C5' substitutions of the agonist ribose ring, making possible more high affinity and subtype selective binding and potentially ligand specific modulation of adenosine receptor function. (nih.gov)

Second, a phenylalanine residue at the center of the ATP pocket strongly affects the ability of the inhibitor to bind to the protein. (rcsb.org)
Our work on intracellular antibody fragments as tools for analysis of protein complexes argued that these macromolecules could also be employed for target validation in diseases and then as guides for target-specific surrogate compounds as inhibitors. (cancer.gov)
We wondered if these difficulties could be overcome by focussing on the antibody combining site (i.e. the part of antibody interacting with antigen) to guide the derivation of chemical compounds that would be surrogates of the antibody, because the combining site is the part relevant to the protein-protein interaction between antibody and antigen. (cancer.gov)
The corollary is that the specific interaction interface between the antibody fragment with target protein would be mimicked by the chemical compound surrogates. (cancer.gov)
Capture Compounds are trifunctional small molecules to reduce the complexity of the proteome by functional reversible small molecule-protein interaction followed by photo-crosslinking and purification. (jove.com)
However, if known active compounds of a target protein are unavailable, the machine learning-based method cannot be applied. (biomedcentral.com)
In this research, we proposed an end-to-end learning-based compound activity prediction using structure information of a binding pocket of a target protein. (biomedcentral.com)
The proposed method learns the important features by end-to-end learning using a graph neural network both for a compound structure and a protein binding pocket structure. (biomedcentral.com)
However, LBVS cannot be applied if we have no compound activity data of a target protein. (biomedcentral.com)
SBVS generally performs a simulation based on physicochemistry using the 3-dimensional structure of a target protein for predicting the activity of a compound. (biomedcentral.com)
Docking simulation needs to search a large conformational space by rotating and translating a compound and calculate the binding energy of a protein-compound interaction using a complicated score function. (biomedcentral.com)
It has been proposed that the metastasis-promoting calcium-binding protein S100P which possesses both intracellular and extracellular functions activates key cell signaling pathways, including MAP kinase and nuclear factor NFκB pathways through its extracellular interaction with the receptor for advanced glycation end products (RAGE). (brighton.ac.uk)
We probe the open conformation of human Hsp90α for druggable sites that overlap with these allosteric control elements, and identify three putative natural compound allosteric modulators: Cephalostatin 17, 20(29)-Lupene-3β-isoferulate and 3′-Bromorubrolide F. We assess the allosteric potential of these ligands by examining their effect on the conformational dynamics of the protein. (nature.com)
Structure-based drug design, in which the physical structure of a targeted protein is used to help identify compounds that will interact with it, has already been used to generate therapeutic agents for a number of infectious and metabolic diseases. (uclahealth.org)
The UCLA researchers, led by David Eisenberg, director of the UCLA-Department of Energy Institute of Genomics and Proteomics and a Howard Hughes Medical Institute investigator, report the first application of this technique in the search for molecular compounds that bind to and inhibit the activity of the amyloid-beta protein responsible for forming dangerous plaques in the brain of patients with Alzheimer's and other degenerative diseases. (uclahealth.org)
Armed with a precise knowledge of the atomic structure of the amyloid-beta protein, Jiang, Eisenberg and colleagues conducted a computational screening of 18,000 compounds in search of those most likely to bind tightly and effectively to the protein. (uclahealth.org)
While these compounds did not reduce the amount of protein aggregates, they were found to reduce the protein's toxicity and to increase the stability of amyloid fibrils - a finding that lends further evidence to the theory that smaller assemblies of amyloid-beta known as oligomers, and not the fibrils themselves, are the toxic agents responsible for Alzheimer's symptoms. (uclahealth.org)
The researchers hypothesize that by binding snugly to the protein, the compounds they identified may be preventing these smaller oligomers from breaking free of the amyloid-beta fibrils, thus keeping toxicity in check. (uclahealth.org)
Paclitaxel protein bound is a microtubular inhibitor (albumin-conjugated formulation) and a natural taxane that prevents depolymerization of cellular microtubules, which results in DNA, RNA, and protein synthesis inhibition. (medscape.com)

Porphyrin levels can be reduced by direct methods or with medications that bind porphyrins. (medscape.com)
The composite porphyrin/TiO 2 films obtained from each of the 11 porphyrins have been exposed to 12 different volatile organic compounds (VOCs), and their respective gas-sensitive properties have been analyzed as a function of the spectral changes in their Soret band region in the presence of the analytes. (us-csic.es)

Achieving absolute specificity, or binding to a single compound exclusively, is challenging due to the structural similarities among molecules. (neoaptamers.com)
Often referred to as "chemical antibodies," these short, single-stranded DNA or RNA sequences possess a remarkable ability to bind to specific target molecules with high affinity. (neoaptamers.com)
Aptamers are molecules that can be engineered to possess specific three-dimensional shapes, enabling them to selectively bind to target molecules. (neoaptamers.com)
However, this process does not account for sequences that exhibit weak binding to non-target molecules. (neoaptamers.com)
The chemical binding between the dye molecules and the TiO 2 has been studied through infrared spectroscopy, and the obtained spectral changes have been found to be compatible with chelating and/or bidentate binding modes of the carboxylate groups on the TiO 2 surface. (us-csic.es)
The green and red molecules are atomic representations of one of the compounds discovered by Jiang, et al. (uclahealth.org)
Directly targeting menaquinone (MK), which plays an important role in bacterial electron transport, is an appealing, yet underexplored, mode of action due to a dearth of MK-binding molecules. (nature.com)
These results indicate that the bound water molecules play a crucial role in the tight interaction between GN 3 M and HEWL. (frontiersin.org)

The aim of this investigation was to find a proper harvesting period and establishing fern number, which effects the spear yield, bioactive compounds and antioxidant activities of Asparagus officinalis L. Spears were harvested at 2, 4, and 6 weeks after sprouting. (nih.gov)
In conclusion, antioxidant status (bioactive compounds, binding and antioxidant activities) improved with the harvesting period and the first segment from spear tip. (nih.gov)
AU - Rasera,Gabriela Boscariol, AU - Hilkner,Marina Hermenegildo, AU - de Castro,Ruann Janser Soares, Y1 - 2020/02/19/ PY - 2019/07/22/received PY - 2020/01/08/revised PY - 2020/02/18/accepted PY - 2020/5/30/entrez PY - 2020/5/30/pubmed PY - 2021/4/1/medline KW - Antioxidant potential KW - Bioactive compounds KW - Brassica nigra KW - Sinapsis alba SP - 109115 EP - 109115 JF - Food research international (Ottawa, Ont. (unboundmedicine.com)

Our initial results highlight 22 new lead compounds that inhibit S100P-RAGE interaction, some of which have shown an ability to decrease pancreatic cell line growth. (brighton.ac.uk)

First, 2 and related compounds bind to an unusual, inactive conformation of the kinase which to the best of our knowledge has not been reported for other types of kinase inhibitors. (rcsb.org)
The thermodynamic data obtained from our study would be useful to understand the substrate binding mechanism of HEWL and to design novel glycosidase inhibitors with moranoline moiety. (frontiersin.org)

Such studies have revealed that polyphenols, naturally occurring compounds found in green tea and in the spice turmeric, can inhibit the formation of amyloid fibrils. (uclahealth.org)

The six nitrate ligands bind as bidentate ligands. (wikipedia.org)
The synthesized compounds were used as ligands in the complexation reactions with bis(triphenylphosphine)nickel(II) and palladium(II) chlorides to give six new metallacomplexes with unusual Î·5:κ1(N)-coordination of the metal center. (bvsalud.org)

In the first Abd technology application, we used a competitive surface plasmon resonance (cSPR) method [9] that depends on high affinity interaction of the antibody fragment with GTP-bound RAS. (cancer.gov)

In soft tissues, phosphate is mainly found in the intracellular compartment as an integral component of several organic compounds, including nucleic acids and cell membrane phospholipids. (msdmanuals.com)

In this study, molecular electrostatic potential (MEP) surfaces of PCP-like compounds are modelled and visualized in order to extract features which will be used in predicting binding affinity. (metu.edu.tr)
In this study, in-silico approaches, including molecular docking and molecular dynamics simulation were applied to investigate binding affinities of 300 alkaloids into the α3β4 (Pdb id: 6PV8). (ijpsr.com)
Molecular dynamics simulations revealed the potential of A128 to binding stably with the α3β4 during 20 ns. (ijpsr.com)
Binding free energy of the complex A128 - α3β4 was calculated based on Molecular Mechanics - Poisson Boltzmann Surface Area (MM-PBSA) method, which also emphasized the importance of electrostatic contacts over van der Waals interactions for proper binding. (ijpsr.com)
UCLA chemists and molecular biologists have for the first time used a "structure-based" approach to drug design to identify compounds with the potential to delay or treat Alzheimer's disease, and possibly Parkinson's, Lou Gehrig's disease and other degenerative disorders. (uclahealth.org)

Based on these factors, it seemed possible that compounds that bind to antigens could be selected using Dab binding sites and that these compounds would be surrogates of the Dab. (cancer.gov)
To allow the immune system to recognize millions of different antigens, the antigen-binding sites at both tips of the antibody come in an equally wide variety. (wikipedia.org)

The chemical compound series that was developed in this work is a pan-RAS series binding to all the RAS isoforms [12] because the binding pocket is found in KRAS, HRAS and NRAS. (cancer.gov)
At the initial stage of drug discovery, a compound screening is often performed for selecting drug candidate compounds from a chemical compound library. (biomedcentral.com)

Surface plasmon resonance (SPR) has not been widely used for compound screening and in this study it was used to compare human and mouse galectin-3 affinity measures between FP and SPR, as well as investigate compound kinetics. (lu.se)

However, the conformation search and the evaluation of binding energy of docking simulation are computationally heavy and thus docking simulation needs huge computational resources. (biomedcentral.com)

Free and insoluble-bound phenolics: How does the variation of these compounds affect the antioxidant properties of mustard grains during germination? (unboundmedicine.com)
This work aimed to investigate how the variation of free and insoluble-bound phenolics affected the antioxidant properties of mustard grains from two varieties (black - Brassica nigra and white - Sinapsis alba) during different germination parameters. (unboundmedicine.com)

Amino Acids is an international peer-reviewed journal dedicated to publishing high-quality research related to the chemistry, biochemistry, physiology, pharmacology, and toxicology of amino acids and related compounds. (springer.com)

Virtual screening is a computational method to predict the activity of chemical compounds without biochemical experiments. (biomedcentral.com)

This technology includes adenosine receptor binding compounds which could potentially be used for development of more selective and safe treatment of cardiovascular, psychiatric and neurodegenerative disorders. (nih.gov)
Selective estrogen receptor (ER) down-regulators (SERDs) are pure ER antagonists that also induce ER degradation upon binding to the receptor. (nih.gov)
It travels in the synaptic cleft and reaches the postsynaptic membrane, where it binds to its receptor (muscarinic or nicotinic). (medscape.com)

disrupts DNA function by covalently binding to DNA bases. (medscape.com)

While CeZ2 compounds are known, they are polychalcogenides with cerium(III): cerium(IV) derivatives of S, Se, and Te are unknown. (wikipedia.org)
The 4f electron in cerocene, Ce(C 8H 8) 2, is poised ambiguously between being localized and delocalized and this compound is also considered intermediate-valent.Alkyl, alkynyl, and alkenyl organocerium derivatives are prepared from the transmetallation of the respective organolithium or Grignard reagents, and are more nucleophilic but less basic than their precursors. (wikipedia.org)
Ultimately, the researchers identified eight compounds and three compound derivatives that had a significant effect. (uclahealth.org)

Compound methods Authentication protocol in which methods are used in a sequence one after another or in which methods are tunneled inside another independently established tunnel between the client and server [TUN-EAP]. (ietf.org)

A ) The location of the different binding site residues are shaded: Site-1 helix 18-19 (red), helix 21-22 four-helix bundle (yellow) and Site-2 sub-pocket (blue). (nature.com)

The top hit compounds were A122 (indole alkaloid) and A128 (tropane alkaloid) with their binding affinities of less than -8.0 kcal.mol -1 and the interactions with key residue, Trp149. (ijpsr.com)
Structures and binding affinities relationships between the indole and tropane compounds with the α3β4 emphasized the important roles of indole backbone and the benzyl substituent at C3 of tropane scaffold in forming the hydrophobic interactions making good binding affinities. (ijpsr.com)
The K D estimates for a set of compounds selected from mono- and di-saccharides with affinities across a 550-fold range, correlated well between FP and SPR assay formats for both human and mouse galectin-3. (lu.se)

In this study, in order to elucidate the driving forces responsible for the tight binding of GN 3 M (a transition-state analogue inhibitor) to HEWL, we conducted a detailed thermodynamic analysis using isothermal titration calorimetry. (frontiersin.org)

A number of non-structural screening attempts have been made to identify natural and synthetic compounds that might prevent the aggregation and toxicity of amyloid fibrils. (uclahealth.org)
Those compounds that showed the strongest potential for binding were then tested for their efficacy in blocking the aggregation of amyloid-beta and for their ability to protect mammalian cells grown in culture from the protein's toxic effects, which in the past has proved very difficult. (uclahealth.org)

Improvements in the field, including the synthesis of this kind of compounds, can contribute to the development of efficient, cheap, and easy-to-prepare anion receptors. (edu.sa)

By means of this procedure, an imagelike recognition pattern has been obtained, which allows an easy identification of every compound. (us-csic.es)

Structure, modes of action, stability, and resistance to these plant compounds will be discussed as well as their application in food industries and possible technologies by which they can be delivered. (hindawi.com)

We propose and theoretically investigate an alternative way to create the poor man's Majorana bound states (MBSs) introduced in Phys. (lu.se)

Mixed infections of fungal trunk pathogens and induced systemic phenolic compound production in grapevines. (usda.gov)

After an antigen binds to a BCR, the B cell activates to proliferate and differentiate into either plasma cells , which secrete soluble antibodies with the same paratope, or memory B cells , which survive in the body to enable long-lasting immunity to the antigen. (wikipedia.org)

Here we combine sequence-based metagenomic mining with a motif search of bioinformatically predicted natural product structures to identify six biosynthetic gene clusters that we predicted encode MK-binding antibiotics (MBAs). (nature.com)

Starting from HTS hit aminopyrazine 2, compounds with improved activity were identified using structure-based design. (rcsb.org)
LBVS predicts the activity of a given compound only from its chemical structure and supervised machine learning algorithms are used for the prediction. (biomedcentral.com)
Upon binding with TC, the configuration of TC-Apt is changed and desorbs from the Ni-HHTP, resulting in the decrease of the nanozyme activity of aptasensor. (bvsalud.org)
Some compounds had higher antiparasitic activity than the parent compound pulchrol, and in some cases even Benznidazole and Miltefosine. (lu.se)

Aptamers can be highly selective, binding to their intended target while ignoring closely related compounds. (neoaptamers.com)

Structurally an antibody is also partitioned into two antigen-binding fragments (Fab), containing one V L , V H , C L , and C H 1 domain each, as well as the crystallisable fragment (Fc), forming the trunk of the Y shape. (wikipedia.org)

The compounds that are found in some spices and produced by herbs act as self-defense mechanisms to protect the plant against infectious organisms [ 3 ]. (hindawi.com)

The compound ceric ammonium nitrate ("CAN") (NH4)2[Ce(NO3)6] is the most common cerium compound encountered in the laboratory. (wikipedia.org)

The execution time of docking simulation of a compound is acceptable. (biomedcentral.com)
Therefore, even if a docking simulation can evaluate one compound in 10 s, a screening of a compound library includin10 million compounds requires approximately 1200 CPU days. (biomedcentral.com)

Increasing regulatory restrictions and consumer negative response to chemical compounds and to the use of antibiotics in agriculture have contributed to the pressure for the development of alternative compounds for use as antimicrobial agents [ 6 ]. (hindawi.com)

For aptamers to be highly specific, researchers must identify unique binding sites on the target molecule, which differentiates it from all other compounds. (neoaptamers.com)
The binding affinity in the blood to the heme which normally carries oxygen reduces the available sites for oxygen. (cdc.gov)
Moreover, indications of some of the possible interactions that may take place in the binding sites were also identified. (lu.se)

Using X-ray crystallography soaking of KRASQ61H crystals by compounds, we implemented a structure-based compound development programme [9, 12]. (cancer.gov)

[2] [3] Each tip of the "Y" of an antibody contains a paratope (analogous to a lock) that is specific for one particular epitope (analogous to a key) on an antigen, allowing these two structures to bind together with precision. (wikipedia.org)

Using this binding mechanism, an antibody can tag a microbe or an infected cell for attack by other parts of the immune system, or can neutralize it directly (for example, by blocking a part of a virus that is essential for its invasion). (wikipedia.org)

organic bases (amines) neutral (esters, ketones, aldehydes, ethers, etc) Organic acids, organic bases, and neutral organic compounds can be readily separated from each other on the basis of their acid-base characteristics. (bartleby.com)

With the growing consumer demand for natural preservatives to replace chemical compounds, plant antimicrobial compounds must be thoroughly investigated for their potential to serve as biopreservatives. (hindawi.com)
There was no significant difference in the binding potential of [ 11 C]DASB between the groups in any of the brain regions examined. (cambridge.org)
The compound action potential (CAP) threshold evoked by pure tone stimuli was used as a measure of auditory sensitivity. (cdc.gov)

Compound hemizygous variants in SERPINA7 gene cause thyroxine-binding globulin deficiency. (illumina.com)

Support vector machines and partial least squares method are used for predicting binding affinity of compounds, and results are compared. (metu.edu.tr)
The docking results showed that most of the alkaloids fitted well into the binding pocket of α3β4. (ijpsr.com)

Historically, the screening and triaging of small molecule glycomimetics that bind to the galectin-3 CRD has been completed in fluorescence polarisation (FP) assays to determine K D values. (lu.se)

We exploited the specific binding of the antibody fragment and were able to identify RAS-binding compounds in antibody-competition assays (illustrated in Fig.1). (cancer.gov)
When the antibody fragment is bound to RAS, it serves as a competitor of compounds binding to the same region. (cancer.gov)
panel B depicts inhibition of this compound by the presence of the anti-RAS antibody fragment). (cancer.gov)

Increases in affinity for compounds binding to human galectin-3 were driven by changes in both k on and k off whilst for mouse galectin-3 this was primarily due to k on . (lu.se)

Anatomy15

Organisms13

Chemicals and Drugs128

Analytical, Diagnostic and Therapeutic Techniques and Equipment40

Phenomena and Processes57

Disciplines and Occupations3

Technology, Industry, Agriculture1

Information Science4

Health Care2

Proteins5

Affinity and selectivity2

Selectivity6

Phenolic compounds1

Ligand4

Protein19

Porphyrins2

Molecules8

Bioactive3

Lead compounds1

Inhibitors2

Polyphenols1

Ligands2

Interaction1

Intracellular1

Molecular5

Antigens2

Chemical compound2

Kinetics1

Conformation1

Antioxidant2

Chemistry1

Computational1

Receptor3

Covalently1

Derivatives3

Methods1

Residues1

Affinities3

Analogue1

Aggregation2

Synthesis1

Identification1

Stability1

Investigate1

Pathogens1

Activates1

Biosynthetic1

Activity4

Selective1

Structurally1

Found1

Laboratory1

Simulation2

Antibiotics1

Sites3

Development1

Structures1

Mechanism1

Bases1

Potential3

Gene1

Results2

Small1

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Driven1