57 results about "Small molecule binding" patented technology

The invention provides a target protein and micromolecule binding prediction method and system. The target protein and micromolecule binding prediction method includes the steps: obtaining physicochemical characteristic data of a protein pocket to be bound and a small molecule to be queried; converting the physicochemical characteristic data of the protein pocket to be bound and the small moleculeto be queried into a pocket vector and a small molecule vector; and respectively inputting the pocket vector and the small molecule vector into a pre-set prediction model based on a deep neural network to obtain a prediction result of the binding probability. The target protein and micromolecule binding prediction method and system extract the active pocket part directly related to the interaction to represent protein, thus being beneficial to removing of non-related information and reduction of noise so as to improve accuracy. In addition, the target protein and micromolecule binding prediction method and system design a neural full-connected layer network model suitable for a learning vector to more easily retain more complete information, and can maintain the key information of the function of the small molecules of the protein by the vector while not depending on the protein small molecule complex conformation for laying the foundation for accurate prediction at high speed.

The present invention relates to a compound represented by a formula (I), antitumor applications and intermediates thereof, and applications of the intermediates, wherein the intermediates are compounds represented by a formula (III) and a formula (IV), the compound represented by the formula (I) has degradation effects on specific target proteins, and mainly comprises three parts, the first partis small molecules binding protein (SMBP), the second part is a link unit (Linker), the third part ubiquitin ligase binding moiety (ULM) is a ligand with ubiquitination function, SMBP and LIN are covalently bound, and LIN is covalently bound to ULM. According to the present invention, a series of the designed and synthesized compounds of the present disclosure have wide pharmacological activities,have function of degradation of specific proteins and / or inhibition of activities, and can be used for related tumor treatment.

The invention relates to a method for testing the total antibody of hepatitis C virus (HCV), based on dual-antibody interlayer method of small-molecule indirect mark, wherein said method is characterized in that: it uses small molecule matter as mark; uses dual-antigen interlayer method to test the total antibody of sample; and said method comprises: using small molecule material to mark HCV antigen; using HCV antigen to pack solid material; using single generate material to mark small molecule antibody or other material that combined with small molecule; the HCV antibody of sample can be reacted with HCV antigen of solid material surface and small molecule mark, to form dual-antigen interlayer composite; then reacting the small molecule with single report molecule, to make the composite with detected signal generate material. The invention can keep activity of antigen, with signal amplifying function and better specificity of dual-antigen interlayer mode, while it can detect variable kinds of antibodies, to improve the detecting sensitivity and specificity.

Described herein is technology for determining the 2-D or 3-D atomic resolution structure of a polynucleotide bound to and / or interacting with another molecule, for example a small molecule. In some aspects of the technology, NMR and isotopic labeling strategies are used. The technology described herein is useful for a plurality of applications including but not limited to drug discovery and chemical biology probe discovery.

Bcl-xL / Bcl-2 binding inhibitors useful in the treatment of unwanted proliferating cells, including cancers and precancers, in subjects in need of such treatment. Also provided are methods of treating a subject having unwanted proliferating cells comprising administering a therapeutically effective amount of a Bcl-xL / Bcl-2 binding inhibitor described herein to a subject in need of such treatment. Also provided are methods of preventing the proliferation of unwanted proliferating cells, such as cancers and precancers, in a subject comprising the step of administering a therapeutically effective amount of a Bcl-xL / Bcl-2 binding inhibitor described herein to a subject at risk of developing a condition characterized by unwanted proliferating cells.

The invention discloses an exonuclease protection analysis based fluorescent biosensor method for detecting single nucleotide polymorphism, which comprises allele-specific extension of micromolecule modified single nucleotide, interaction between an oligonucleotide DNA strand primer with micromolecules after extension and binding protein, protection analysis of the exonuclease III / I and fluorescent quantitative detection of a hairpin type oligonucleotide DNA probe primer subjected to end protection based on double-strand indicating dye. The method adopts allele-specific extension of the primer to combine the micromolecule modified single nucleotide at 3' end of a specific primer and then combine the specificity of the binding protein of the micromolecule to protect the primer from being degraded by the exonuclease III / I, and detects single nucleotide polymorphism genotyping through fluorescence of the complex of the protected oligonucleotide DNA primer and double-strand inserting dye. The method features simple and convenient operation, economy, fast speed, sensitivity and strong specificity and is expected to provide a universal technology platform for screening and prenatal diagnosis of the population suffering from gene mutation related genetic diseases.

Provided herein are libraries of scaffolds derived from riboswitches and small ribozymes and their methods of use. The scaffolds of the invention yield aptamers that are easily identified and characterized by virtue of the structural scaffold. The nature of the scaffold predisposes these RNAs for coupling to readout domains to engineer biosensors that function in vitro and in vivo. Biosensors, synthetic RNA agents and synthetic DNA agents, and their methods of use, are also provided.

The invention relates to a method for testing the total antibody of hepatitis C virus (HCV), based on dual-antibody interlayer method of small-molecule indirect mark, wherein said method is characterized in that: it uses small molecule matter as mark; uses dual-antigen interlayer method to test the total antibody of sample; and said method comprises: using small molecule material to mark HCV antigen; using HCV antigen to pack solid material; using single generate material to mark small molecule antibody or other material that combined with small molecule; the HCV antibody of sample can be reacted with HCV antigen of solid material surface and small molecule mark, to form dual-antigen interlayer composite; then reacting the small molecule with single report molecule, to make the composite with detected signal generate material. The invention can keep activity of antigen, with signal amplifying function and better specificity of dual-antigen interlayer mode, while it can detect variable kinds of antibodies, to improve the detecting sensitivity and specificity.

A new class of activated polyalkylene glycol acids and their active ester reagents for conjugation to biopharmaceuticals such as polypeptides, sugars, proteins and therapeutically active small molecules to produce biologically active conjugates of these pharmaceuticals and methods for producing these conjugates.

The invention relates to the field of biology, and discloses a compound for recognizing a notched G-quadruplex, and a preparation method and application of the compound. The compound for recognizing the notched G-quadruplex comprises a guanine molecule and a polypeptide or a small molecule capable of recognizing the G-quadruplex, wherein the polypeptide or the small molecule is connected with theguanine molecule through an amido bond, and the structural formula of the compound is shown in the specification. In the structural formula, R1 or R2 is the small molecule or the polypeptide. According to the compound for recognizing the notched G-quadruplex provided by the invention, a notch is filled with guanine to form a hydrogen bond, and the polypeptide or the small molecule is combined witha guanine plane at the tail end of the notched G-quadruplex so as to allow two binding sites to exist between the polypeptide or the small molecule and the notched G-quadruplex, so the notched G-quadruplex can be specifically recognized, the stability of the notched G-quadruplex can be improved, and the DNA replication inhibition ability of the notched G-quadruplex can be enhanced.

The invention relates to a targeted mesoporous molecular imaging probe and a preparation method thereof. The targeted mesoporous molecular imaging probe comprises two parts including a surface plasma resonance core layer and a peripheral coating layer, wherein the surface plasma resonance core layer at least comprises a gold nanorod I, a gold nanorod II and substrate nano particles; the peripheral coating layer is formed by fluorescent molecules, sulfydryl small biological molecules and polystyrene sulfonate connectors; the gold nanorod I and the gold nanorod II are cohered on the substrate nano particles, so that the surface plasma resonance core layer can be formed; the distance between the gold nanorod I and the gold nanorod II meets the condition that d is more than or equal to (r1-r2) / 2 and less than or equal to (r1+r2) / 2; the exterior of the core layer is combined with the sulfydryl small biological molecules by a gold sulfhydryl bond, the fluorescent molecules are combined with the sulfydryl small biological molecules by an amide covalent bond, and polystyrene sulfonate is directly connected on a substrate in a bridging way. The invention also provides the preparation method of the targeted mesoporous molecular imaging probe. Blue shift or red shift is generated by surface excitation, and the characteristics of luminescence of a fluorescent structure are matched, so that the brightness is increased by 8-10 orders of magnitude. The targeted mesoporous molecular imaging probe has very high fluorescence characteristic, thus being applied to the diagnosis of tumor fluorescence imaging; the targeted mesoporous molecular imaging probe is especially suitable for detection and diagnosis of tumors in the dark field at the deep part of tissue cells.

The invention relates to a method for identifying key flexible amino acids on a protein small molecule binding pockets. The method comprises the following steps: step 1, in a protein PDB structure, classifying the protein structure into different subtype clusters through 95% sequence similarity; step 2, overlapping all protein structures in the subtype cluster with the same structure by using a clear biological ligand, and accurately identifying small molecule binding pockets on the protein; step 3, dividing the corresponding binding sites in the same structure subtype cluster of the known 3Dstructure into site binding subtypes according to the binding positions of small molecules; step 4, researching the protein flexibility property by calculating physicochemical and structural parameterdifference characterization factors; and step 5, identifying key flexible residues by using the highest score of a system for forming the protein binding pockets. A set of uniform and unbiased research process system is designed, and a set of systematic mathematical statistical formula is developed to determine the structural flexibility of binding site amino acids at the same position of different structural models.

This invention relates to methods for the evaluation and / or quantification of the binding affinity of small molecules or other compounds to target components contained within an analyte, such as target proteins contained within the proteome of a cell or tissue.