The First Insight into the Tissue Specific Taxus Transcriptome via Illumina Second Generation Sequencing

The First Insight into the Tissue Specific Taxus Transcriptome via Illumina Second Generation SequencingBackground: Illumina second generation sequencing is now an efficient route for generating enormous sequence collections that represent expressed genes and quantitate expression level. Taxus is a world-wide endangered gymnosperm genus and forms an important anti-cancer medicinal resource, but the large and complex genomes of Taxus have hindered the development of genomic resources. The research of its tissue-specific transcriptome is absent. There is also no study concerning the association between the plant transcriptome and metabolome with respect to the plant tissue type

Optical substrates for drug-metabolizing enzymes : Recent advances and future perspectives

Drug-metabolizing enzymes (DMEs), a diverse group of enzymes responsible for the metabolic elimination of drugs and other xenobiotics, have been recognized as the critical determinants to drug safety and efficacy. Deciphering and understanding the key roles of individual DMEs in drug metabolism and toxicity, as well as characterizing the interactions of central DMEs with xenobiotics require reliable, practical and highly specific tools for sensing the activities of these enzymes in biological systems. In the last few decades, the scientists have developed a variety of optical substrates for sensing human DMEs, parts of them have been successfully used for studying target enzyme(s) in tissue preparations and living systems. Herein, molecular design principals and recent advances in the development and applications of optical substrates for human DMEs have been reviewed systematically. Furthermore, the challenges and future perspectives in this field are also highlighted. The presented information offers a group of practical approaches and imaging tools for sensing DMEs activities in complex biological systems, which strongly facilitates high-throughput screening the modulators of target DMEs and studies on drug/herb-drug interactions, as well as promotes the fundamental researches for exploring the relevance of DMEs to human diseases and drug treatment outcomes. (C) 2022 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V.Peer reviewe

Target Enzyme-Activated Two-Photon Fluorescent Probes:A Case Study of CYP3A4 Using a Two-Dimensional Design Strategy

The rapid development of fluorescent probes for monitoring target enzymes is still a great challenge owing to the lack of efficient ways to optimize a specific fluorophore. Herein, a practical two-dimensional strategy was designed for the development of an isoform-specific probe for CYP3A4, a key cytochrome P450 isoform responsible for the oxidation of most clinical drugs. In first dimension of the design strategy, a potential two-photon fluorescent substrate (NN) for CYP3A4 was effectively selected using ensemble-based virtual screening. In the second dimension, various substituent groups were introduced into NN to optimize the isoform-selectivity and reactivity. Finally, with ideal selectivity and sensitivity, NEN was successfully applied to the real-time detection of CYP3A4 in living cells and zebrafish. These findings suggested that our strategy is practical for developing an isoform-specific probe for a target enzyme.</p

High fat diet significantly changed the global gene expression profile involved in hepatic drug metabolism and pharmacokinetic system in mice.

Background: High fat diet impact transcription of hepatic genes responsible for drug metabolism and pharmacokinetics. Until now, researches just focused on a couple specific genes without a global profile showing. Age-dependent manner was also not noted well. This study aims to investigate the high fat diet effect on transcriptome of drug metabolism and pharmacokinetic system in mouse livers and show the age-dependent evidence. Methods: C57BL/6 male mice were used in this experiment. High fat diet was used to treat mice for 16 and 38 weeks. Serum total cholesterol, low density lipoprotein cholesterol, aspartate transaminase, and alanine transaminaselevels were measured. Meanwhile, Histology, RNA-Seq, RT-PCR analysis and fourteen major hepatic bile acids quantification were performed for the liver tissues. Data was mined at levels of genes, drug metabolism and pharmacokinetic sysem, and genome wide. Results: Treatment with high fat diet for 38 weeks significantly increased levels of serum lipids as well as aspartate transaminase, and alanine transaminase. Meanwhile, lipid accumulation in livers was observed. At week 38 of the experiment, the profile of 612 genes involved in drug metabolism and pharmacokinetics was significantly changed, indicated by a heatmap visulization and a principal component analysis. In total 210 genes were significantly regulated. Cyp3a11, Cyp4a10, and Cyp4a14 were down-regulated by 10-35 folds, while these three genes also were highly expressed in the liver. High fat diet regulated 11% of genome-wide gene while 30% of genes involved in the hepatic drug metabolism and pharmacokinetic system. Genes, including Conclusions: High fat diet changed the global transcription profile of hepatic drug metabolism and pharmacokinetic system with a age-dependent manner

Molecular Design Strategy to Construct the Near-Infrared Fluorescent Probe for Selectively Sensing Human Cytochrome P450 2J2

Cytochrome P450 2J2 (CYP2J2), a key enzyme responsible for oxidative metabolism of various xenobiotics and endogenous compounds, participates in a diverse array of physiological and pathological processes in humans. Its biological role in tumorigenesis and cancer diagnosis remains poorly understood, owing to the lack of molecular tools suitable for real-time monitoring CYP2J2 in complex biological systems. Using molecular design principles we were able to modify the distance between the catalytic unit and metabolic recognition moiety, allowing us to develop a CYP2J2 selective fluorescent probe using a near-infrared fluorophore (E)-2-(2-(6-hydroxy-2, 3-dihydro-1H-xanthen-4-yl)vinyl)-3,3- dimethyl-1-propyl-3H-indol-1-ium iodide (HXPI). To improve the reactivity and isoform specificity, a self-immolative linker was introduced to the HXPI derivatives in order to better fit the narrow substrate channel of CYP2J2, the modification effectively shortened the spatial distance between the metabolic moiety (O-alkyl group) and catalytic center of CYP2J2. After screening a panel of O-alkylated HXPI derivatives, BnXPI displayed the best combination of specificity, sensitivity and applicability for detecting CYP2J2 in vitro and in vivo. Upon O-demethylation by CYP2J2, a self-immolative reaction occurred spontaneously via 1,6-elimination of p-hydroxybenzyl resulting in the release of HXPI. Allowing BnXPI to be successfully used to monitor CYP2J2 activity in real-time for various living systems including cells, tumor tissues, and tumor-bearing animals. In summary, our practical strategy could help the development of a highly specific and broadly applicable tool for monitoring CYP2J2, which offers great promise for exploring the biological functions of CYP2J2 in tumorigenesis.</p

Molecular Design Strategy to Construct the Near-Infrared Fluorescent Probe for Selectively Sensing Human Cytochrome P450 2J2

Cytochrome P450 2J2 (CYP2J2), a key enzyme responsible for oxidative metabolism of various xenobiotics and endogenous compounds, participates in a diverse array of physiological and pathological processes in humans. Its biological role in tumorigenesis and cancer diagnosis remains poorly understood, owing to the lack of molecular tools suitable for real-time monitoring CYP2J2 in complex biological systems. Using molecular design principles, we were able to modify the distance between the catalytic unit and metabolic recognition moiety, allowing us to develop a CYP2J2 selective fluorescent probe using a near-infrared fluorophore (E)-2-(2-(6-hydroxy-2, 3-dihydro-1H-xanthen-4-yl)­vinyl)-3,3-dimethyl-1-propyl-3H-indol-1-ium iodide (HXPI). To improve the reactivity and isoform specificity, a self-immolative linker was introduced to the HXPI derivatives in order to better fit the narrow substrate channel of CYP2J2, the modification effectively shortened the spatial distance between the metabolic moiety (O-alkyl group) and catalytic center of CYP2J2. After screening a panel of O-alkylated HXPI derivatives, BnXPI displayed the best combination of specificity, sensitivity and applicability for detecting CYP2J2 in vitro and in vivo. Upon O-demethylation by CYP2J2, a self-immolative reaction occurred spontaneously via 1,6-elimination of p-hydroxybenzyl resulting in the release of HXPI. Allowing BnXPI to be successfully used to monitor CYP2J2 activity in real-time for various living systems including cells, tumor tissues, and tumor-bearing animals. In summary, our practical strategy could help the development of a highly specific and broadly applicable tool for monitoring CYP2J2, which offers great promise for exploring the biological functions of CYP2J2 in tumorigenesis

DeepSeek LLM: Scaling Open-Source Language Models with Longtermism

The rapid development of open-source large language models (LLMs) has been truly remarkable. However, the scaling law described in previous literature presents varying conclusions, which casts a dark cloud over scaling LLMs. We delve into the study of scaling laws and present our distinctive findings that facilitate scaling of large scale models in two commonly used open-source configurations, 7B and 67B. Guided by the scaling laws, we introduce DeepSeek LLM, a project dedicated to advancing open-source language models with a long-term perspective. To support the pre-training phase, we have developed a dataset that currently consists of 2 trillion tokens and is continuously expanding. We further conduct supervised fine-tuning (SFT) and Direct Preference Optimization (DPO) on DeepSeek LLM Base models, resulting in the creation of DeepSeek Chat models. Our evaluation results demonstrate that DeepSeek LLM 67B surpasses LLaMA-2 70B on various benchmarks, particularly in the domains of code, mathematics, and reasoning. Furthermore, open-ended evaluations reveal that DeepSeek LLM 67B Chat exhibits superior performance compared to GPT-3.5

Recent progress and challenges in screening and characterization of UGT1A1 inhibitors

Uridine-diphosphate glucuronosyltransferase 1A1 (UGT1A1) is an important conjugative enzyme in mammals that is responsible for the conjugation and detoxification of both endogenous and xenobiotic compounds. Strong inhibition of UGT1A1 may trigger adverse drug/herb-drug interactions, or result in metabolic disorders of endobiotic metabolism. Therefore, both the US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) have recommended assaying the inhibitory potential of drugs under development on the human UGT1A1 prior to approval. This review focuses on the significance, progress and challenges in discovery and characterization of UGT1A1 inhibitors. Recent advances in the development of UGT1A1 probes and their application for screening UGT1A1 inhibitors are summarized and discussed in this review for the first time. Furthermore, a long list of UGT1A1 inhibitors, including information on their inhibition potency, inhibition mode, and affinity, has been prepared and analyzed. Challenges and future directions in this field are highlighted in the final section. The information and knowledge that are presented in this review provide guidance for rational use of drugs/herbs in order to avoid the occurrence of adverse effects via UGT1A1 inhibition, as well as presenting methods for rapid screening and characterization of UGT1A1 inhibitors and for facilitating investigations on UGT1A1-ligand interactions. (C) 2019 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V.Peer reviewe

Identification of human UDP-glucuronosyltransferase isoforms involved in the isofraxidin glucuronidation and assessment of the species differences of the reaction

Isofraxidin, 7-Hydroxy-6.8-dimethoxy-2H-1-benzopyran-2-one, is a major active component of Acanthopanax senticosus, which has been used as Acanthopanax (Ciwujia) injection to treat cardiovascular and cerebrovascular diseases in China for more than thirty years. The purpose of this study was to identify the roles of human UDP-glucuronosyltransferases (UGTs) in isofraxidin glucuronidation in the liver and intestinal microsomes and to reveal the potential species differences by comparing the liver microsomal glucuronidation from different experimental animals. One metabolite was biosynthesized and characterized as isofraxidin-7-O-glucuronide by liquid chromatography tandeirt mass spectrometry (LC-MS/MS) and nuclear magnetic resonance (NMR). The intrinsic clearances in human liver and intestinal microsomes were 63.8 and 16.4 mu L/min/mg, respectively. Human liver microsomes displays higher potential for isofraxidin elimination than human intestinal microsomes. The reaction phenotyping analysis Was conducted using cDNA-expressed human UGTs and chemical inhibitors. The results indicated that UGT1A1 and UGT1A9 were the main isoforms involved in the formation of isofraxidin-7-O-glucuronide. The isofraxidin glucuronidation in liver microsomes from human (HLM), rat (RLM), mouse (MLM), dog (DLM), monkey (CyLM), minipig (PLM), and guinea pig (GpLM) followed the Michealis-Menten model. The isofraxidin glucuronidation displays species differences in terms of catalytic activities. GpLM had the highest clearance with the CLint value of 152 mu L/min/mg. CyLM, RLM and MLM exhibit similar catalytic activities in isofraxidin glucuronidation with the intrinsic clearance values of 54.6, 58.0 and 50.2 mu L/min/mg, respectively, which are higher than those of PLM and DLM (23.9 and 37.7 mu L/min/mg, respectively). Rat exhibits the most similar intrinsic metabolic clearance (CLint) to human. (C) 2016 Published by Elsevier B.V

Study of a series of fluorophore-labeled artesunate derivatives Design, analysis and application

Artesunate (ART) Is an antimalarial and potential anticancer drug which exerts diverse physiological and pathological functions. Unfortunately, the detailed mechanisms of operation of ART derivatives still remain elusive. To solve this, modification of ART with fluorophores can be a good choice. However, whether the modification has any influence on the drug itself is still a problem that remains to be solved. Herein, three different fluorophores (anthracene (E), pyrene (B) and naphthalimide (N)) were designed and synthesized to covalently link with ART to get three fluorophore-labeled ART derivatives (AE, AB and AN). The result demonstrated that the spectral characteristics of these derivatives was not affected by different fluorophores. While, AN cannot be hydrolyzed by the most common drug metabolism enzymes like human liver microsomes (HLM), rat liver microsomes (RLM) and mouse liver microsomes (MLM). In comparison, AE and AB can be hydrolyzed much easier than AN, leading to the release of ART. Co localization studies suggest that AN exhibited superior lysosome-targeting ability than AE and AB, due to the preferential accumulation of ART in lysosome and the remarkable enzyme hydrolysis stability of AN. Furthermore, not much cytotoxicity was observed for the corresponding fluorophore-labeled ART derivatives compared with that of ART alone. (C) 2017 Elsevier Ltd. All rights reserved