1306 results about "Target protein" patented technology

The invention discloses a protein palmitoyl transferase prediction method and system based on a multi-branch deep convolutional neural network, and belongs to the technical field of bioinformatics and artificial intelligence. The method comprises the following steps: S1, obtaining a to-be-detected protein sequence; s2, inputting the protein sequence into a pre-trained iPalmT model; and S3, judging whether the target protein is palmitoyl transferase or not according to a model output result. The iPalmT model comprises a coding module, two paths of parallel convolution branches, a feature fusion module and a classification module; and after the convolution layers of each convolution branch are stacked, an SE module is arranged and is used for channel weighting and feature re-calibration. The model extracts multi-level sequence features through convolution kernels of different scales, realizes high-precision prediction through feature fusion and a residual structure, can automatically learn multi-scale features from large-scale data, realizes end-to-end palmitoyl transferase recognition, and has high accuracy and good universality.

The invention discloses an mRNA non-coding region sequence optimization method and system and electronic equipment, and the mRNA non-coding region sequence optimization method comprises the steps: constructing an initial candidate library according to a target protein; inputting the initial candidate library into a pre-trained mRNA sequence optimization model to obtain a prediction data set; performing multi-dimensional scoring and sequence optimization on the prediction data set to obtain a sequence recommendation group; performing biological verification on the sequence recommendation group to obtain an optimized mRNA sequence; wherein the prediction data set comprises a sequence ID, a sequence content, a prediction TE score and a confidence interval. According to the method, the translation efficiency of the mRNA sequence can be efficiently and accurately predicted, the candidate sequence with high expression potential is screened out, meanwhile, the consumption of computing resources is reduced, and the overall design cost is reduced.

Provided are compounds that may bind a target protein, and result in modification of the target protein. The compounds may further bind a modifier protein. The modifier protein may carry out or enhance the modification of the target protein. The modification may activate or reactivate the target protein. Also provided are methods of using the compounds.

The invention provides a double-target degradation molecule based on a functionalized nucleic acid connexon and application thereof, and relates to the technical field of biological medicine, the double-target degradation molecule comprises an E3 ubiquitin ligase ligand at one end, a first target protein ligand at the other end, and the functionalized nucleic acid connexon located between the E3 ubiquitin ligase ligand and the first target protein ligand; the functionalized nucleic acid linker is a nucleotide sequence capable of specifically recognizing and combining a second target protein or a coding gene thereof, so that the protein level degradation of the first target protein and the nucleic acid level or expression level inhibition of the second target protein / gene are realized in the same molecule. Functionalized nucleic acid and a PROTAC strategy are organically combined, single-molecule double-target collaborative intervention is achieved, targeting efficiency and treatment potential are improved, higher flexibility and expandability are provided in synthesis and design, and a new molecular platform and technical route are provided for multi-target accurate treatment.

The invention discloses a novel benzofuran component in eupatorium chinense and application of the benzofuran component in anti-inflammatory activity. The obtained compound is separated from an eupatorium chinense extract. The eupatorium chinense root extract is separated by using an extraction method, macroporous adsorption resin impurity removal, Sephadex LH-20 gel column chromatography, high performance liquid chromatography and other methods. According to the present invention, all the separated compounds and the analogues thereof have good inhibition activity on target cyclooxygenase-2 of inflammation-related diseases, and have good inhibition activity on COX-2 enzyme, and the molecular docking experiment results show that the compounds and the target proteins have good binding energy. Therefore, the compound can be used for preparing drugs for treating inflammatory related diseases, or anti-inflammatory and analgesic drugs, or tumor drugs by inhibiting COX-2 enzyme, such as drugs for rheumatoid arthritis, osteoarthritis, ankylosing spondylitis, Alzheimer's disease and the like, and related natural lead compounds are provided.

The invention belongs to the field of medical technology analysis, and discloses an analysis method and system for revealing a hidden binding pocket of a drug target, and the method comprises the steps: firstly obtaining a representative conformation metastable state of a target protein through conventional molecular dynamics simulation and clustering analysis; secondly, constructing a Markov state model to analyze a dynamic transformation rule between conformations; carrying out enhanced sampling by adopting meta-dynamics, and deeply exploring a rare conformation space; and finally, constructing a free energy landscape to quantitatively evaluate the relative stability of the conformation, and identifying a hidden binding pocket in the stable rare conformation. According to the method, the limitation of a single calculation means is overcome, a full-chain calculation system of dynamic conformation analysis-hidden cavity feature mining-novel ligand rational design is constructed, and the formation mechanism and potential druggability of the hidden pocket can be comprehensively revealed from the two dimensions of dynamics and thermodynamics; and an efficient and accurate calculation framework is provided for research and development of innovative drugs targeting difficult drug targets.

The invention discloses a chimera for degrading a CARD structural domain protein aggregate and application of the chimera. The chimera is prepared from light-operated targeting protein and light-operated degradation protein, the light-operated targeting protein is sequentially connected by an MAVS CARD structural domain, a flexible connecting peptide and a photosensitive protein pMag; the light-controlled degradation protein is sequentially connected by a photosensitive protein nMag, a flexible connecting peptide and an RING structural domain of TRIM21. According to the application, a light-operated activated CARD-RING chimera is constructed, and when the CARTAC generates toxic and side effects or in cells with RIG-I / MDA5 signal channels abnormally activated, the activity of the CARTAC can be effectively controlled or autoimmune diseases caused by RIG-I / MDA5 abnormity can be inhibited.

The invention provides a cell protein degradation platform based on an artificial biological macromolecular aggregate. Specifically, the invention provides a PROTAC functional module based on an interworking nucleic acid skeleton, a PROTAC-aggregate complex (MLO-PROTAC), a kit, application and a preparation method of the PROTAC functional module, the PROTAC-aggregate complex (MLO-PROTAC) and the kit, and also provides a targeted protein degradation method. In a PROTAC platform built by the PROTAC functional module and the PROTAC-aggregate complex, a programmable nucleic acid component is used as a core assembly unit, and the functional module is enriched and spatiotemporal-spatial regulation is performed by using the polypeptide aggregate, so that the delivery efficiency and the cytoplasm exposure degree are remarkably improved while the universality is maintained, and the delivery efficiency and the cytoplasm exposure degree are remarkably improved. Therefore, a more effective target protein degradation way is provided for the field.

Disclosed herein are predictive models for T-cell epitope prediction, B-cell epitope prediction, and protein design wherein a method is implemented for generating a protein variant amino acid sequence of a target protein having one or more modified properties, the method comprising: (a) iteratively sampling an input amino acid sequence of the target protein, and (b) sampling the individual protein score of at least one weighted relative contribution of the single residue mutant input amino acid sequence to the at least one target property across a plurality of other single residue mutant input amino acid sequences to generate a combined protein score, wherein the combined protein score corresponds to the protein variant comprising one or more amino acid mutations of the single residue mutant input amino acid sequences.

The invention provides a disease marker epitope prediction and antibody screening method, which belongs to the technical field of disease markers, and comprises the following steps: firstly, establishing a training data set containing a known antigen-antibody compound structure and disease tissue expression data; and obtaining target protein sequence information through liquid chromatography-mass spectrometry analysis and carrying out sequence comparison. And then a deep convolutional neural network is utilized to extract sequence features, and surface exposure sites are identified by combining secondary structure prediction and solvent accessibility analysis. After the features are integrated with sequence evolution conservative properties, a prediction model is constructed by using a random forest classifier. The method comprises the following steps: carrying out molecular dynamics simulation on a prediction result, screening first 10% of candidate sequences through a comprehensive scoring function and K-means clustering, and finally determining an antigen epitope sequence with the strongest binding activity through verification of an antigen chip and a fluorescence labeled antibody system, so that the technical problem that specific antigen epitopes are difficult to accurately predict and recognize in the prior art is solved.

The invention belongs to the technical field of biological medicine, and particularly relates to an engineered cell microvesicle and a delivery system based on the engineered cell microvesicle, the system realizes efficient preparation of 1-5 [mu] m cell microvesicles, and the cell microvesicles have a large space volume and can be used for preparing the cell microvesicles. The carrier can be used for loading and delivery of target protein, polypeptide and recombinase which are specifically expressed in mother cells. The system transfects mother cells through lentivirus transfection or plasmid transfection to further produce cell microvesicles, and the microvesicles can load more goods and inherit membrane proteins of the mother cells, and can also effectively load intracellular proteins to realize effective delivery. By virtue of good structural stability, high immunogenicity and excellent biocompatibility, the cell microvesicle reduces systematic toxic and side effects of a traditional carrier, is expected to become an effective drug delivery system, and has great application potential in the field of gene therapy.

The invention discloses application of a target protein circPIAS1-108aa inhibitor combined with oxaliplatin in preparation of a medicine synergistic composition for treating cancers, the specific action mechanism of circPIAS1-108aa in colon cancer treatment is found for the first time, and further research shows that by using siRNA to knock down circPIAS1-108aa, colon cancer cell proliferation can be remarkably inhibited, and the effect of treating the colon cancer can be achieved. Furthermore, the target spot protein circPIAS1-108aa inhibitor can be used for enhancing the treatment effect of the oxaliplatin. Therefore, when the circPIAS1-108aa expression is inhibited in a targeted manner and the oxaliplatin is combined for use, the circPIAS1-108aa can be obviously used for preventing and treating cancers, the dosage and toxic and side effects of the oxaliplatin are reduced, and a new synergistic strategy is provided for tumor treatment.

The invention provides antibody conjugate compositions of Formula I comprising an antibody linked by conjugation to one or more target protein binder and VHL ligand (TPI-VHL) moieties. The invention also provides TPI-VHL derivative intermediate compositions comprising a reactive functional group. Such intermediate compositions are suitable substrates for formation of the antibody conjugates through a linker or linking moiety. The invention further provides methods of treating diseases and disorders such as cancer with the antibody conjugates.

The invention discloses a method for improving the solubility and thermal stability of sweet protein, and belongs to the technical field of biosynthesis, the method comprises the following steps: constructing a gene tandem recombinant plasmid containing a monellin x-3C-sfGFP-3C-monellin y expression cassette, x is greater than or equal to 1, y is greater than or equal to 1, 5 is greater than or equal to x + y is greater than or equal to 3, a 3C protease recognition sequence is also inserted between adjacent copies of monellin, and each monellin is connected with a purification tag; the gene tandem recombinant plasmid is transformed into escherichia coli and inducible expression is carried out, thalli are split and purified to obtain fusion protein, 3C protease is used for enzyme digestion, and the target protein is obtained after re-purification. The total protein yield and the solubility proportion are remarkably improved by adopting a series construction mode of plasmids, meanwhile, the stability of monellin is effectively improved, the purification step is simpler and more convenient, and the method is suitable for industrial production.

The invention discloses a nanoparticle for targeted protein degradation and a degradation method. The nanoparticles can enhance uptake of cells and effectively encapsulate specific antibodies for recognizing target proteins, and meanwhile, the interferon component can induce expression of TRIM family proteins in the cells. After ingestion into the cell, the antibody released by the nanoparticle can bind to the target protein and bind to the TRIM family protein to mediate degradation of the target protein. In this process, although the TRIM family protein is continuously consumed, the TRIM family protein can be compensated by the TRIM family protein expression induced by the particle of the invention, thereby maintaining efficient degradation.

The invention discloses a drug delivery system based on branched chain nucleic acid as well as a preparation method and application of the drug delivery system. The drug delivery system comprises a multivalent nucleic acid framework, a nucleic acid-small molecule coupling drug and a nucleic acid-polypeptide coupling drug, a nucleic acid nanostructure is formed through base complementary pairing assembly, and the nucleic acid-small molecule coupling drug comprises first nucleic acid and an E3 ubiquitin ligase ligand coupled with the first nucleic acid; the nucleic acid-polypeptide coupling drug comprises a second nucleic acid and a cell penetrating peptide coupled with the second nucleic acid. The drug delivery system disclosed by the invention can respond to a tumor microenvironment, so that cell penetrating peptides are activated, tumor penetrating and cytoplasm delivery capacities are enhanced, the aim of efficiently degrading tumor-related target proteins is fulfilled by combining a multivalent effect, and a remarkable tumor treatment effect is achieved; in addition, the preparation method is simple and easy to implement, has universality and high production efficiency, and is expected to be applied to treatment of various tumors.

The present invention relates to a novel regulatory element. The regulatory element according to one embodiment is capable of increasing RNA stability or mRNA translation of a transcription product of a target gene, thereby being capable of increasing the expression level of the target protein, and can be effectively used in systems requiring precise control of gene expression, such as gene therapy, vaccine development, and production of protein therapeutics. Furthermore, the regulatory element of the present application exhibits excellent stability-increasing ability and translation-regulating ability not only in unmodified RNA but also in RNA containing a modified base, and thus can be effectively used in therapeutic mRNA or vaccine platforms requiring base modification.

The present disclosure relates to a novel class of bifunctional molecules that are useful in a targeted or selective degradation of a protein.

The invention discloses a functional protein screening method based on a large language model, and belongs to the technical field of protein screening, and the method specifically comprises the following steps: obtaining a protein three-dimensional structure and functional literature, converting the protein three-dimensional structure and functional literature into a multi-modal feature vector by using an encoder, and constructing a domain-specific vector database; after a screening instruction is received, related feature data of semantic matching is called through a vector retrieval algorithm; then, inputting the data into a large language model to execute biological mechanism reasoning, and outputting an initial candidate protein sequence containing predicted activity; further, physical binding energy is calculated by using a molecular docking program, a deviation coefficient between the physical binding energy and the predicted activity is generated, and the coefficient is used as a penalty term to construct a dynamic correction function to update the scoring weight; and finally, performing secondary sorting on the candidate set based on the updated weight, and outputting the sequence sorted for the first time as a target protein. According to the method, AI reasoning and physical verification are effectively combined, and the screening accuracy is improved.

The invention provides a drug target prediction method based on cross-modal attention and uncertainty evaluation, and belongs to the technical field of drug target prediction. In order to solve the technical problems that the existing drug target prediction lacks quantitative evaluation on the reliability of a prediction result and a nonlinear interaction relationship between a drug and a target is difficult to establish, the method comprises the following steps: collecting data, and fusing graph structure features and sequence features of extracted drug molecules to obtain a final code of the drug molecules; extracting amino acid sequence characteristics of the target protein, and constructing protein sequence characteristic expression; inputting the drug molecular features and the protein sequence features into a cross-modal attention module, and aligning and fusing the drug features and the protein features by using a bidirectional cross attention mechanism to obtain drug-target combined feature representation; introducing an uncertainty quantification mechanism, and outputting uncertainty estimation of a drug-target interaction prediction label and a prediction result; the method is used for predicting drug target interaction.

The invention discloses a construction method and application of a probiotic engineering bacterium EcNpAm targeting animal intestinal tracts and improving inflammation. According to the present invention, the heterologous expression of the immunomodulatory protein Amuc1100 is successfully achieved through the gene engineering technology by using the Escherichia coli Niss1917 (EcN) as the host and using the anaerobic inducible plasmid pnirBMisL as the expression vector, and the novel engineering bacterium EcNpAm suitable for the animal intestinal anaerobic environment is constructed; furthermore, the expression efficiency of the target protein is represented by fusion expression of green fluorescent protein (GFP). The engineering bacterium is applied to prevention and treatment of animal intestinal inflammation, and successfully realizes targeted delivery of therapeutic protein to intestinal tracts of mice. Experiments show that EcNpAm can effectively relieve typical symptoms such as weight loss, colon shortening, pathological injury, colitis and the like of mice induced by dextran sodium sulfate (DSS) and protect integrity and functions of an intestinal barrier structure.

The invention discloses a pseudomonas aeruginosa InA protein and application thereof, and relates to the technical field of biological detection, the InA protein is InAS2, InAAP41 or InAS8, the amino acid sequences of the InA protein are respectively shown as SEQ ID NO.1-3, and the nucleotide sequences for coding the InAS2, the InAAP41 and the InAS8 are shown as SEQ ID NO.4-6. Compared with the prior art, the InA protein can improve the solubility of target protein, in addition, the InA protein and pseudomonas aeruginosa immune protein also have ultrahigh affinity, a biosensing chip with regeneration reversibility is developed based on the InA protein, the chip can capture fusion protein with the InA protein, and the biosensing chip has the advantages that the biosensing chip can be used as a biosensing chip with regeneration reversibility, so that the biosensing chip can be applied to biosensing of pseudomonas aeruginosa. The chip can be used for detecting the affinity between the fusion protein with the InA tag and a candidate drug, drug screening is realized, and meanwhile, the protein-drug affinity kinetics detected by the chip can also be used for pharmacological research of drugs.

The invention belongs to the technical field of medical chemistry, and particularly relates to a targeted protein degradation compound containing an SYVN1 binding compound and application of the targeted protein degradation compound. According to the invention, a series of compounds interacting with SYVN1 are found, and the compounds can be used as'warheads' to participate in ERAD and effectively degrade transmembrane protein targets. Based on the SYVN1 binding compound, a new TPD technology for hijacking ERAD is established, and a brand new platform is provided for processing TMSPs and other proteins which are difficult to target by the current TPD technology. A SYVN1 interaction compound is further connected with a known ligand interacting with a protein target through a chemical linker, a series of ERADEC molecules are generated, the molecules can significantly degrade target protein, and a new possibility is provided for targeted degradation of drugs.

The invention relates to the technical field of bioinformatics, and discloses an iterative feedback type protein targeting molecule intelligent generation method and device, and the method comprises the steps: obtaining molecular structure data, training based on the molecular structure data to obtain a molecular fragment language model, and the molecular fragment language model is used for predicting subsequent molecular fragments according to an input molecular fragment sequence; obtaining an attribute preference data set, and performing alignment fine tuning on the pre-trained molecular fragment language model based on the attribute preference data set to obtain an attribute preference alignment model; and obtaining target structure information of the target protein, taking the attribute preference alignment model as a strategy network, iteratively generating and evaluating candidate molecules through a tree search algorithm under the constraint of the target structure information until a termination condition is met, and outputting the optimized protein targeting molecules. According to the application, excellent pharmacological properties can be taken into account while the protein targeting molecule binding effect is ensured, and the molecule generation quality can be dynamically optimized.

The invention discloses a protein quantitative detection method which comprises the following steps: respectively constructing a capture probe for capturing antibody coupling magnetic beads and oligonucleotides and a detection probe for detecting antibody coupling oligonucleotides through a biorthogonal chemical coupling method; then, target protein is captured by using a biorthogonal chemical coupling and magnetic bead sandwich method comprising the steps of capture probe combination, closing, washing, detection probe combination and the like, and accurate quantification of low-abundance protein in a complex sample is realized by combining a subsequent digital PCR (Polymerase Chain Reaction) technology.

The present invention provides compounds, compositions thereof, and methods of using the same for the targeted degradation of proteins, and the treatment of target protein-mediated disorders.

The invention discloses application of benzofuran components in eupatorium chinense to reduction of uric acid, compounds 1-3 are obtained by being separated from an eupatorium chinense extract, and the compound 1 is a new compound. The eupatorium chinense root extract is separated by using an extraction method, macroporous adsorption resin impurity removal, HW-40F gel column chromatography, high performance liquid chromatography and other methods to obtain the benzofuran compound. According to the present invention, the inhibition activity of the gout disease related target xanthine oxidase of the separated compound 1-3 is tested, the experimental result shows that the compound 1-3 has good inhibition activity on the xanthine oxidase, and the molecular docking experiment shows that the compound 1-3 has good binding energy with the target protein. Therefore, the compounds 1-3 can be used for preparing a natural lead compound for delaying or treating diseases caused by xanthine oxidase and providing a natural lead compound in the field of treatment of hyperuricemia and gout.

The invention belongs to the field of biological medicine, and relates to a guide agRNA for regulating RNA splicing. The invention provides an application of a guide agRNA (Ribonucleic Acid) in preparation of a medicine for changing expression of a target protein by cells of a subject. The guide agRNA recruits ADAR protein to the 3 'splice site or pseudo 3' splice site to edit the A base of the 3 'splice site or pseudo 3' splice site, thereby splicing the whole exon located at the 3 'splice site or flanking the pseudo 3' splice site of the intron from the precursor mRNA, thereby changing the level of mRNA encoding the target protein, and altering the expression of the target protein in the cell. The target gene pre-mRNA selective splicing is regulated and controlled to influence the function or expression of the functional RNA and the target protein of the target gene, so that the purpose of treating diseases is achieved.

A target protein drug binding prediction method based on meta learning and subgraph matching, by constructing protein structure, drug small molecule structure and its binding energy value, the meta learning training task is established according to protein grouping, that is, as the main model of the meta model; the sub model and its loss function for the protein prediction task are obtained after fine tuning of the meta model; then the task self-adaptive self-attention model is established to balance the optimization contribution of the sub model of each protein prediction task to the meta model, the weighted average is used for the loss function of the sub model of each protein prediction task to obtain the meta model loss function; then the meta model loss function is used to calculate the gradient, the meta model parameters are updated and optimized based on the preset learning rate, and after the training is completed, the trained meta model is used for fine tuning of the test set of new protein samples, the prediction sub model of the new protein is obtained, the sub model is used for prediction of the protein test set, and the evaluation result is obtained. The training method combining meta learning and subgraph matching can effectively avoid shortcut learning, enhance the generalization effect, and also solve the problem that the previous prediction model is difficult to predict the newly discovered protein.

The present invention relates to an artificial hybrid promoter, and more particularly, to an artificial hybrid promoter including an upstream activation sequence of GAL10 gene and a core promoter sequence of PGK gene, a recombinant expression vector including same, a host cell, and a method of producing a target protein using the host cell.