ABSTRACT
Understanding the research methods for drug protein targets is crucial for the development of new drugs, clinical applications of drugs, drug mechanisms, and the pathogenesis of diseases. Cellular thermal shift assay (CETSA), a target research method without modification, has been widely used since its development. Now, there are various CETSA-based technology combinations, such as mass spectrometry-based cellular thermal shift assay (MS-CETSA), isothermal dose response-cellular thermal shift assay (ITDR-CETSA), amplified luminescent proximity homogeneous assay-cellular thermal shift assay (Alpha-CETSA), etc., which combine their respective advantages and further expand the application scope of CETSA. These technologies are suitable for the entire drug development chain, from drug screening to monitoring the target binding and off-target toxicity of drugs in patients. Based on the author's research experience, this paper reviews the principles of CETSA and related binding technologies, their application in target discovery, and the progress of data processing and analysis in recent years, aiming to provide reference and reference for the further application of CETSA.
ABSTRACT
Single cell RNA sequencing (scRNA-seq) is an advanced technology to study the transcriptome information at the single cell level. The application of this technology can attribute to analyze the heterogeneous map of cells in the process of disease development, and precisely identify the specific cell subsets that are responsive to pharmacological therapy. Currently, scRNA-seq technology has been widely applied in the field of drug research, including studies on therapeutic targets, drug-induced adverse reactions, drug resistance and vaccine. This work reviews the application of scRNA-seq technology in drug discovery, which offers a scientific basis for personalized and accurate medication therapy.
ABSTRACT
The discovery of drug targets plays a crucial role in drug research. Accurate information of small molecule drug-protein interaction can be provided by label-free target discovery technology without any structural modification at the small molecule. So, the label-free drug target discovery technology had become the powerful tool to discover the targets of drugs. Due to the “multi-component and multi-target” characteristics of traditional Chinese medicines (TCMs), the research on its targets and mechanism had been restricted. Based on potential of the label-free target discovery technology in the research of TCMs, this paper summarized the label-free target discovery technology and its application in TCMs research. It will provide a reference for the discovery of targets of TCMs and a new view for promoting the modernization of TCMs.
ABSTRACT
Metabolic regulation is an important mechanism by which organisms adapt to changes in the internal and external environment. Metabolic small molecules function as versatile messengers involved in signaling networks and organ crosstalk, which carries great implications for understanding physiological processes, revealing disease mechanisms and discovering drug targets. In this review, we present an overview of the main progresses in metabolic regulation and drug target discovery researches in China, and look forward to its future direction, which may provide a reference for the drug development endeavor based on metabolic regulation.
ABSTRACT
Drug target discovery is the basis of drug screening.It elucidates the cause of disease and the mechanism of drug action,which is the essential of drug innovation.Target discovery performed in biological sys-tems is complicated as proteins are in low abundance and endogenous compounds may interfere with drug binding.Therefore,methods to track drug-target interactions in biological matrices are urgently required.In this work,a Fe3O4 nanoparticle-based approach was developed for drug-target screening in biofluids.A known ligand-protein complex was selected as a principle-to-proof example to validate the feasibility.After incubation in cell lysates,ligand-modified Fe3O4 nanoparticles bound to the target protein and formed complexes that were separated from the lysates by a magnet for further analysis.The large surface-to-volume ratio of the nanoparticles provides more active sites for the modification of chemical drugs.It enhances the opportunity for ligand-protein interactions,which is beneficial for capturing target proteins,especially for those with low abundance.Additionally,a one-step magnetic separation simplifies the pre-processing of ligand-protein complexes,so it effectively reduces the endogenous interference.Therefore,the present nanoparticle-based approach has the potential to be used for drug target screening in biological systems.
ABSTRACT
Co-citations of foreign and domestic highly cited papers on drug target discovery were analyzed by clustering analysis using BICOMB2.01 and gCLUTO.Semantic analysis of the titles and abstracts in these highly cited papers and their important source literature showed that general trend, theoretical foundation, main methods and principal resources are the major hotspots of text mining in drug target discovery.
ABSTRACT
This review presents a historical overview of drug discovery and the non-clinical stages of the drug development process, from initial target identification and validation, through in silico assays and high throughput screening (HTS), identification of leader molecules and their optimization, the selection of a candidate substance for clinical development, and the use of animal models during the early studies of proof-of-concept (or principle). This report also discusses the relevance of validated and predictive animal models selection, as well as the correct use of animal tests concerning the experimental design, execution and interpretation, which affect the reproducibility, quality and reliability of non-clinical studies necessary to translate to and support clinical studies. Collectively, improving these aspects will certainly contribute to the robustness of both scientific publications and the translation of new substances to clinical development.
Subject(s)
Animals , Computer Simulation , Drug Discovery , Drug Evaluation, Preclinical/methods , Computer-Aided Design , Models, Animal , Reproducibility of ResultsABSTRACT
Objective To explore the optimal proteolysis condition for the new technology of target discovery, drug affinity responsive target stability (DARTS). Methods First, in order to determine the suitable pronase concentration range for DARTS, the extraction of human acute T lymphoblastic leukemia cells (Jurkat) were digested with a range of pronase concentrations (the mass ratio of pronase to protein was 1: 100 to 1: 10000) at room temperature and detected by SDS-PAGE and Coomassie brilliant blue staining. On this basis, in order to obtain the optimal proteolysis condition, we performed DARTS on α-ketoglutarate in combination with SDS-PAGE and gel staining, and observed the effect of different concentrations of pronase (1: 500-1: 5000) and different proteolysis time (5-30 min) on DARTS. The feasibility of the optimum condition was verified by using it on a target known small molecule, mycophenolic acid. Results When the protein extraction of Jurkat was hydrolyzed by a range of pronase concentrations, it was entirely hydrolysed by pronase 1: 100 while showing no significant effect under the condition of pronase 1: 10000. The effect of pronase 1: 500 to 1: 5000 on protein mixture was milder. And approximately 30%-60% of the protein was digested. The protein bands which were protected by α-ketoglutarate could be observed apparently under the conditon of pronase 1: 1000 when the proteolysis time was about 15 min. Then we performed DARTS on mycophenolic acid utilizing this condition (pronase 1: 1000, hydrolysed for 15 min) and obtained several visible protected protein bands between (4-7) ×104. Western blotting results showed that the target protein of mycophenolic acid, IMPDH1, was contained in the protected protein bands. Conclusion The optimal proteolysis condition for DARTS on protein mixture through α-ketoglutarate is obtained.
ABSTRACT
Objective To explore the optimal proteolysis condition for the new technology of target discovery ,drug affinity responsive target stability(DARTS). Methods First,in order to determine the suitable pronase concentration range for DARTS,the extraction of human acute T lymphoblastic leukemia cells(Jurkat)were digested with a range of pronase concentrations(the mass ratio of pronase to protein was 1∶100 to 1∶10000)at room temperature and detected by SDS-PAGE and Coomassie brilliant blue stain?ing. On this basis,in order to obtain the optimal proteolysis condition,we performed DARTS onα-ketoglutarate in combination with SDS-PAGE and gel staining,and observed the effect of different concentrations of pronase(1∶500-1∶5000)and different proteolysis time(5-30 min)on DARTS. The feasibility of the optimum condition was verified by using it on a target known small molecule ,myco?phenolic acid. Results When the protein extraction of Jurkat was hydrolyzed by a range of pronase concentrations,it was entirely hy?drolysed by pronase 1∶100 while showing no significant effect under the condition of pronase 1∶10000. The effect of pronase 1∶500 to 1∶5000 on protein mixture was milder. And approximately 30%-60%of the protein was digested. The protein bands which were protected byα-ketoglutarate could be observed apparently under the conditon of pronase 1∶1000 when the proteolysis time was about 15 min. Then we performed DARTS on mycophenolic acid utilizing this condition(pronase 1∶1000,hydrolysed for 15 min)and obtained sev?eral visible protected protein bands between(4-7)×104. Western blotting results showed that the target protein of mycophenolic acid , IMPDH1,was contained in the protected protein bands. Conclusion The optimal proteolysis condition for DARTS on protein mix?ture throughα-ketoglutarate is obtained.
ABSTRACT
In the post-genomic era, biological studies are characterized by the rapid development and wide application of a series of "omics" technologies, including genomics, proteomics, metabolomics, transcriptomics, lipidomics, cytomics, metallomics, ionomics, interactomics, and phenomics. These "omics" are often based on global analyses of biological samples using high through-put analytical approaches and bioinformatics and may provide new insights into biological phenomena. In this paper, the development and advances in these omics made in the past decades are reviewed, especially genomics, transcriptomics, proteomics and metabolomics; the applications of omics technologies in pharmaceutical research are then summarized in the fields of drug target discovery, toxicity evaluation, personalized medicine, and traditional Chinese medicine; and finally, the limitations of omics are discussed, along with the future challenges associated with the multi-omics data processing, dynamics omics analysis, and analytical approaches, as well as amenable solutions and future prospects.