丹参酮生物合成途径及其相关酶的研究进展

丹参酮是丹参中具有多种药理活性的二萜醌类化合物,对预防和治疗心脑血管系统疾病有显著效果。因其具有重要的经济和药用价值,丹参酮的生物合成研究受到人们的广泛关注。随着丹参基因组和转录组数据的不断积累和完善,以及丹参遗传转化体系的建立和基因编辑技术的应用,丹参酮的生物合成途径解析及相关酶基因研究取得了新进展。现系统阐述丹参酮的生物合成途径与研究进展,同时对合成途径相关酶基因的研究现状进行概述,并展望未来的研究方向。     

CYP3A基因表达与调控的分子机制

Ｐ４５０３Ａ是参与药的氧化代谢的重要酶系,在肝脏及肠道中含量丰富。人体内参与药物代谢的ＣＹＰ３Ａ亚系为ＣＹＰ３Ａ４、ＣＹＰ３Ａ５、ＣＹＰ３Ａ７。其中ＣＹＰ３Ａ７主要存在于胚胎肝脏。ＣＹＰ３Ａ的主要调控位于５端,其中某些转录调控因子结合位点与ＣＹＰ３Ａ在组织中的特异性表达有关。５端有两个特殊结构ＮＦＳＥ与ＨＦＬａＳＥ分别为ＣＹＰ３Ａ４与ＣＹＰＡ３Ａ７所独有,可能与基分别在成人及胚胎计中的特异性表达有     

氯吡格雷对大鼠肝药物酶CYP3A4 和CYP1A2 表达的影响

目的：氯吡格雷主要由CYP3A4 催化使其激活,CYP1A2 也参与氯吡格雷活化。关于氯吡格雷对肝微粒体酶的影响国内外 文献报道不多,因此本实验通过检测肝细胞色素氧化酶CYP3A4 和CYP1A2 的表达,探讨氯吡格雷对大鼠肝药物酶的影 响。方法：生理盐水为对照组,氯吡格雷设高、中、低三个剂量组（27,13.5,6.75mg/kg/d）,雄性健康大鼠连续灌胃给药7天,脱臼处 死,取肝组织,通过western blot法检测大鼠肝脏CYP3A4 和CYP1A2 蛋白表达情况。结果：1）、氯吡格雷抑制大鼠CYP3A4 蛋白 表达,氯吡格雷高中低剂量组分别比生理盐水组大鼠CYP3A4 蛋白表达量降低（P<0.05）;氯吡格雷低中高剂量组间进行比较,大 鼠CYP3A4 蛋白表达量呈梯度减少（P<0.05）;2）、氯吡格雷抑制大鼠CYP1A2 蛋白表达,氯吡格雷高中低剂量组分别比生理盐水 组大鼠CYP1A2 蛋白表达量降低（P<0.05）,氯吡格雷低中高剂量组间进行比较,大鼠CYP1A2 蛋白表达量呈梯度减少（P<0.05）。 结论：氯吡格雷使肝细胞色素氧化酶CYP3A4 和CYP1A2 的表达量减少,因此氯吡格雷高、中、低3 个剂量组均不同程度的抑制 大鼠肝脏CYP3A4 和CYP1A2 的表达,提示当氯吡格雷与某些主要经CYP3A4 和CYP1A2 代谢的药物合用时,发生代谢性相关 作用的可能性大。     

氯吡格雷对大鼠肝药物酶CYP3A4和CYP1A2表达的影响

目的：氯吡格雷主要由CYP3A4催化使其激活,CYPlA2也参与氯吡格雷活化。关于氯吡格雷对肝微粒体酶的影响国内外文献报道不多,因此本实验通过检测肝细胞色素氧化酶CYP3A4和CYPlA2的表达,探讨氯吡格雷对大鼠肝药物酶的影响。方法：生理盐水为对照组,氯吡格雷设高、中、低三个剂量组（27,13．5,6．75mg／kg／d）,雄性健康大鼠连续灌胃给药7天,脱臼处死,取肝组织,通过westernblot法检测大鼠肝脏CYP3A4和CYPlA2蛋白表达情况。结果：1）、氯吡格雷抑制大鼠CYP3A4蛋白表达,氯吡格雷高中低剂量组分别比生理盐水组大鼠CYP3A4蛋白表达量降低（P〈0．05）;氯吡格雷低中高剂量组间进行比较,大鼠CYP3A4蛋白表达量呈梯度减少（P〈0．05）;2）、氯吡格雷抑制大鼠CYPlA2蛋白表达,氯吡格雷高中低剂量组分别比生理盐水组大鼠CYPlA2蛋白表达量降低（P〈0．05）,氯吡格雷低中高剂量组间进行比较,大鼠CYPlA2蛋白表达量呈梯度减少（P〈0．05）。结论：氯吡格雷使肝细胞色素氧化酶CYP3A4和CYPlA2的表达量减少,因此氯吡格雷高、中、低3个剂量组均不同程度的抑制大鼠肝脏CYP3A4和CYPlA2的表达,提示当氯吡格雷与某些主要经CYP3A4和CYPlA2代谢的药物合用时,发生代谢性相关作用的可能性大。     

基于TCMSP数据库的分子对接虚拟筛选JAK3特异性抑制剂CSCD

以LeDock分子对接软件对TCMSP数据库中的13445种中草药成分小分子与JAK3激酶进行分子模拟对接研究,分析对接结合自由能与配体效率,筛选出18种小分子,再根据受体与配体的相互作用进一步分析,得到7种与JAK3激酶有较好结合作用的小分子,并且发现JAK3激酶分子中氨基酸残基Arg953、Asp967、Lys830、Ala966和Asn954是小分子与酶形成氢键作用的重要位点,为JAK3抑制剂的开发设计提供有力依据。以其他JAK家族成员为靶蛋白,进行反向筛选,发现断马钱子苷(scologanin)对JAK3激酶表现出强结合力与高选择性。本研究意在寻找可以作为JAK3激酶高选择性抑制剂的中草药药效小分子,结果发现断马钱子苷具备相应的潜力,值得进一步深入研究。     

基于分子对接技术的抗新型冠状病毒三叶青化合物虚拟筛选

利用分子对接技术探索三叶青中对新型冠状病毒(severe acute respiratory syndrome coronavirus 2,SARS-CoV-2)有潜在抑制作用的活性化合物.通过检索国内外文献,搜集到162个三叶青化合物,同时与瑞德西韦、利托那韦和奈非那韦3个化学药建立配体库,并以3CL水解酶蛋白(3C...     

米曲霉木糖醇脱氢酶的分子模建与对接

[目的]研究米曲霉木糖醇脱氢酶基因的结构与功能.[方法]克隆测序来源于米曲霉的木糖醇脱氢酶(XDH)基因,利用Swiss-MODEL和Modeller对XDH进行三级结构模建,通过PROCHECK和Prosa2003对得到的4个目标模型进行评价,从中得到一个最佳模型.在同源建模的基础上,通过分子对接软件MolsoftICM-Pro,对辅因子进行对接,预测了XDH与NAD+、Zn2+作用的相关残基.寻找底物木糖醇与XDH结合的可能活性口袋,用Molsoft模拟XDH与木糖醇的对接,预测了酶与底物作用的关键氨基酸残基.[结果]结构分析显示,米曲霉XDH含有醇脱氢酶家族锌指纹结构和典型醇脱氢酶Rossmann折叠的辅酶结合域,属于Medium-chain脱氢酶(MDR)家族.通过对接研究,预测了XDH与NAD+之间形成氢键的氨基酸有Asp206、Arg211、Ser255、Ser301和Arg303,这些氨基酸位于结合域,与Zn2+形成氢键的氨基酸有His72和Glu73,位于催化域,与天然底物木糖醇形成氢键的氨基酸有Ile46、Ile349、Lys350和Thr351,位于催化域.[结论]所得信息对XDH分子定向改造、拓展米曲霉工业应用范围有重要意义.     

玉米黑粉菌CYP51稀有密码子和mRNA二级结构分析及与杀菌剂戊唑醇分子对接

通过截短玉米黑粉菌CYP51(P450-14DM,UmCYP51)基因(去除编码跨膜区部分)和选取不同的表达载体,构建了9种重组表达质粒,在大肠杆菌中进行UmCYP51基因的表达,发现只有BL21(DE3)/pET32-Um-35重组表达工程菌获得了表达.对稀有密码子和mRNA翻译起始区二级结构进行分析,结果表明稀有密码子和mRNA翻译起始区二级结构对UmCYP51蛋白的表达都有影响.适用于稀有密码子表达的菌株Rosetta(DE3)不利于UmCYP51蛋白的表达;同时只有翻译起始区二级结构自由能值最低的重组载体pET32-Um-35可以表达.为了设计以UmCYP51为靶标的新型抗真菌抑制剂,基于最新解析的真核生物人类的CYP51晶体结构,利用同源模建的方法构建了UmCYP51的三维结构并进行了分子动力学模拟优化.通过与商品化杀菌剂戊唑醇进行分子对接获得了此类抑制剂与UmCYP51的理论结合方式,阐述了戊唑醇分子的杀菌机理,为开发新型的抗真菌抑制剂奠定了基础.     

中国汉族急性白血病患儿化疗药物不良反应与CYP3A5*3的关联性研究

目的:探讨中国汉族儿童CYP3A5*3与白血病药物不良反应的关联.方法:入选2004年7月至2011年6月间确诊的急性白血病儿童52名,用PCR-RFLP方法测定CYP3A5*3突变,同时收集病人常规资料和不良反应.结果:白血病儿童主要不良反应为呕吐、口腔黏膜损害、一过性骨髓抑制、肝功能损害.且CYP3A5*3/*3病人相对于其他两组,更易于发生白细胞减少和粘膜损害.结论:CYP3A5*3与病人的不良反应发生密切相关,可作为白血病治疗效果预测基因.     

铁皮石斛甘露糖结合凝聚素的分子建模与对接研究

本文通过序列分析获得了铁皮石斛甘露糖结合凝聚素(Dendrobium officinale mannose-binding lectin,DOL)成熟肽和甘露糖结合位点(50-58AA,81-89AA,116-124AA)。通过同源建模建立了DOL三维结构模型,DOL呈中空的三棱柱结构,三棱柱的三个侧面主要由β折叠构成,三个侧面各有一个甘露糖结合部位。甘露糖与DOL的分子对接和动力学分析表明,结合位点50-58AA和81-89AA对甘露糖的结合要强于116-124AA,在与甘露糖结合的过程中发挥关键作用的氨基酸残基为Gln81,Asp83,Asn85和Tyr89。研究结果有助于进一步开展凝集素抗病机理及凝集素相关药物研究。     

Studies on Pidotimod Enantiomers With Chiralpak‐IA: Crystal Structure,Thermodynamic Parameters and Molecular Docking

Pidotimod, a synthetic dipeptide, has two chiral centers with biological and immunological activity. Its enantiomers were characterized by x‐ray crystallographic analysis. A chiral stationary phase (CSP) Chiralpak‐IA based on amylose derivatized with tris‐(3, 5‐dimethylphenyl carbamate) was used to separate pidotimod enantiomers. The mobile phase was prepared in a ratio of 35:65:0.2 of methyl‐tert‐butyl‐ether and acetonitrile trifluoroaceticacid. In addition, thermodynamics and molecular docking methods were used to explain the enantioseparation mechanism by Chiralpak‐IA. Thermodynamic studies were carried out from 10 to 45 °C. In general, both retention and enantioselectivity decreased as the temperature increased. Thermodynamic parameters indicate that the interaction force between the pidotimod enantiomer (4S, 2'R) and IA CSP is stronger and their complex model is more stable. According to GOLD molecular docking simulation, Van der Waals force is the leading cause of pidotimod enantiomers separation by IA CSP. Chirality 27:802–808, 2015. © 2015 Wiley Periodicals, Inc.     

蛋白质-蛋白质分子对接方法中分子柔性处理与近天然结构筛选的研究

蛋白质-蛋白质分子对接方法是研究蛋白质分子间相互作用与识别的重要理论方法。该方法主要涉及复合物结合模式的构象搜索和近天然结构的筛选两个问题。在构象搜索中,分子柔性的处理是重点也是难点,围绕这一问题,近年来提出了许多新的方法。针对近天然结构的筛选问题,目前主要采用三种解决策略:结合位点信息的利用、相似结构的聚类和打分函数对结构的评价。本文围绕以上问题,就国内外研究进展和本研究小组的工作作详细的综述,并对进一步的研究方向进行了展望。     

Regulation and induction of CYP3A11, CYP3A13 and CYP3A25 in C57BL/6J mouse liver

This study reports that dexamethasone (DEX) significantly induces CYP3A11, CYP3A13 and CYP3A25 mRNA expression in male and female 4 days, 3 weeks and 18 weeks old C57BL/6J mice. Furthermore, CYP3A activity, as measured by erythromycin-N-demethylation, is also significantly increased. PXR, RXRalpha and CAR are known to be involved in the induction of CYP3As. Here we report nuclear receptors PXR and RXRalpha but not CAR demonstrate gender- and age-dependent expression. Also, treatment of C57BL/6J mice with DEX induces PXR but not RXRalpha or CAR. In summary, we demonstrate DEX is not only able to up-regulate CYP3A expression and activity, but also the nuclear receptor PXR through which it may exert this effect. Furthermore, the gender- and age-dependent pattern of basal PXR and RXRalpha expression is similar to the 3 CYP3As analysed.     

Rapid screening the potential mechanism-based inhibitors of CYP3A4 from Tripterygium wilfordi based on computer approaches combined with in vitro bioassay

CYP3A4 is the main human metabolizing enzyme, and many clinically relevant drug/herb-drug interactions (DDIs/HDIs) involving CYP3A4 are due to mechanism-based inhibition. In this study, pharmacophore model together with molecular docking (MD) are used to rapidly screen the potential CYP3A4 mechanism-based inhibitors from Tripterygium wilfordii, and in vitro experiments are conducted to validate the computational data. The results showed that the rate of computational prediction could be improved based on a combination of pharmacophore model and MD, and a combination of computational approaches might be a useful tool to identify potential mechanism-based inhibitor of CYP3A4 from herbal medicines.     

Comparative study of the interaction mechanism of astilbin,isoastilbin, and neoastilbin with CYP3A4

The interactions of human CYP3A4 with three selected isomer flavonoids, such as astilbin, isoastilbin and neoastilbin, were clarified using spectral analysis, molecular docking, and molecular dynamics simulation. During binding with the three flavonoids, the intrinsic fluorescence of CYP3A4 was statically quenched in static mode with nonradiative energy conversion. The fluorescence and ultraviolet/visible (UV/vis) data revealed that the three flavonoids had a moderate and stronger binding affinity with CYP3A4 due to the order of the K_a1 and K_a2 values ranging from 10⁴ to 10⁵ L·mol⁻¹. In addition, astilbin had the highest affinity with CYP3A4, then isoastilbin and neoastilbin, at the three experimental temperatures. Multispectral analysis confirmed that binding of the three flavonoids resulted in clear changes in the secondary structure of CYP3A4. It was found from fluorescence, UV/vis and molecular docking analyses that these three flavonoids strongly bound to CYP3A4 by means of hydrogen bonds and van der Waals forces. The key amino acids around the binding site were also elucidated. Furthermore, the stabilities of the three CYP3A4 complexes were evaluated using molecular dynamics simulation.     

N‐[2‐[(3‐Chlorophenyl)amino]‐phenyl]‐3‐(difluoromethyl)‐1‐methyl‐1H‐pyrazole‐4‐carboxamide: Synthesis,Crystal Structure,Molecular Docking and Biological Activities

In continuation of our previous research on the development of novel pyrazole‐4‐carboxamide with potential antifungal activity, compound SCU2028 , namely N‐[2‐[(3‐chlorophenyl)amino]phenyl]‐3‐(difluoromethyl)‐1‐methyl‐1H‐pyrazole‐4‐carboxamide, was synthesized by new method, structurally characterized by IR, HR‐ESI‐MS, ¹H‐ and ¹³C‐NMR spectra and further identified by single‐crystal X‐ray diffraction. In pot tests, compound SCU2028 showed good in vivo antifungal activity against Rhizoctonia solani (R. solani) and IC₅₀ value of it was 7.48 mg L^?1. In field trials, control efficacy of compound SCU2028 at 200 g.a.i. ha^?1 was 42.30 % on the 7^th day after the first spraying and 68.10 % on the 14^th day after the second spraying, only slightly lower than that of thifluzamide (57.20 % and 71.40 %, respectively). Further in vitro inhibitory activity showed inhibitory ability of compound SCU2028 was 45‐fold higher than that of bixafen and molecular docking of compound SCU2028 to SDH predicted its binding orientation in the active site of the target protein SDH. These results suggested that compound SCU2028 was a potential fungicide for control of rice sheath blight.     

Allosteric Regulation of 3CL Protease of SARS-CoV-2 and SARS-CoV Observed in the Crystal Structure Ensemble

The 3C-like protease (3CL^pro) of SARS-CoV-2 is a potential therapeutic target for COVID-19. Importantly, it has an abundance of structural information solved as a complex with various drug candidate compounds. Collecting these crystal structures (83 Protein Data Bank (PDB) entries) together with those of the highly homologous 3CL^pro of SARS-CoV (101 PDB entries), we constructed the crystal structure ensemble of 3CL^pro to analyze the dynamic regulation of its catalytic function. The structural dynamics of the 3CL^pro dimer observed in the ensemble were characterized by the motions of four separate loops (the C-loop, E-loop, H-loop, and Linker) and the C-terminal domain III on the rigid core of the chymotrypsin fold. Among the four moving loops, the C-loop (also known as the oxyanion binding loop) causes the order (active)–disorder (collapsed) transition, which is regulated cooperatively by five hydrogen bonds made with the surrounding residues. The C-loop, E-loop, and Linker constitute the major ligand binding sites, which consist of a limited variety of binding residues including the substrate binding subsites. Ligand binding causes a ligand size dependent conformational change to the E-loop and Linker, which further stabilize the C-loop via the hydrogen bond between the C-loop and E-loop. The T285A mutation from SARS-CoV 3CL^pro to SARS-CoV-2 3CL^pro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CL^pro seems to have increased activity relative to that of SARS-CoV 3CL^pro.     

Design and Construction of Aroyl‐Hydrazone Derivatives: Synthesis,Crystal Structure,Molecular Docking and Their Biological Activities

Here, we report the synthesis and characterization of four new aroyl‐hydrazone derivatives L₁ – L₄ , and their structural as well as biological activities have been explored. In addition to docking with bovine serum albumin (BSA) and duplex DNA, the experimental results demonstrate the effective binding of L₁ – L₄ with BSA protein and calf thymus DNA (ct‐DNA) which is in agreement with the docking results. Further biological activities of L₁ – L₄ have been examined through molecular docking with different proteins which are involved in the propagation of viral or cancer diseases. L₁ shows best binding affinity with influenza A virus polymerase PB2 subunit (2VY7) with binding energy ?11.42 kcal/mol and inhibition constant 4.23 nm , whereas L₂ strongly bind with the hepatitis C virus NS5B polymerase (2WCX) with binding energy ?10.47 kcal/mol and inhibition constant 21.06 nm . Ligand L₃ binds strongly with TGF‐beta receptor 1 (3FAA) and L₄ with cancer‐related EphA2 protein kinases (1MQB) with binding energy ?10.61 kcal/mol, ?10.02 kcal/mol and inhibition constant 16.67 nm and 45.41 nm , respectively. The binding energies of L₁ – L₄ are comparable with binding energies of their proven inhibitors. L₁ , L₃ and L₄ can be considered as both 3FAA and 1MQB dual targeting anticancer agents, while L₁ and L₃ are both 2VY7 and 2WCX dual targeting antiviral agents. On the other side, L₂ and L₄ target only one virus related target (2WCX). Furthermore, the geometry optimizations of L₁ – L₄ were performed via density functional theory (DFT). Moreover, all four ligands ( L₁ – L₄ ) were characterized by NMR, FT‐IR, ESI‐MS, elemental analysis and their molecular structures were validated by single crystal X‐ray diffraction studies.     

In Silico Structural Studies and Molecular Docking Analysis of Delta6-desaturase in HUFA Biosynthetic Pathway

Fish are an important source of highly unsaturated fatty acids (HUFA) such as eicosapentaenoic acid EPA (20:5 n-3) and docosahexaenoic acid DHA (22:6 n-3) and play a significant role in human nutrition. The fatty acyl delta6-desaturase (Δ6 desaturase) is a rate-limiting enzyme in the biosynthetic pathway of highly unsaturated fatty acids (HUFA) that converts polyunsaturated fatty acids (PUFA) such as linoleic (18:2n-6) and α-linolenic (18:3n-3) acids into HUFA. In this study, fatty acyl Δ6 desaturase was identified from pangasius (Pangasianodon hypophthalmus) and further analyzed for sequenced-based characterization and 3D structural conformation. Sequenced-based analysis revealed some important secondary information such as physicochemical property. e.g., isoelectric point, extinction coefficient, aliphatic index, and grand average hydropathy, among others, and also post-translational modification sites were identified. An evolutionary-conserved stretch of amino acid residue and a functionally significant conserved structural ancestor, N-terminal cytochrome b5 and membrane FADS-like superfamily, were identified. Protein association analysis showed a high confidence score with acyl-CoA synthetase, elovl5, elovl2, and phospholipase A2. Herein, we report, for the first time, a 3D native structure of Δ6 desaturase protein by homology modeling approach; molecular docking analysis was performed with linoleic (18:2n-6) and α-linolenic (18:3n-3) acids, which are the two key substrates in the HUFA biosynthetic pathway. This work provides insight into the structural and functional characterization of Δ6 desaturase, which is involved in HUFA biosynthesis as a rate-limiting enzyme.     

Crystal Structure of NLRP3 NACHT Domain With an Inhibitor Defines Mechanism of Inflammasome Inhibition

The NLRP3 inflammasome assembles in response to a variety of pathogenic and sterile danger signals, resulting in the production of interleukin-1β and interleukin-18. NLRP3 is a key component of the innate immune system and has been implicated as a driver of a number of acute and chronic diseases. We report the 2.8 Å crystal structure of the NLRP3 NACHT domain in complex with an inhibitor. The structure defines a binding pocket formed by the four subdomains of the NACHT domain, and shows the inhibitor acts as an intramolecular glue, which locks the protein in an inactive conformation. It provides further molecular insight into our understanding of NLRP3 activation, helps to detail the residues involved in subdomain coordination within the NLRP3 NACHT domain, and gives molecular insights into how gain-of-function mutations de-stabilize the inactive conformation of NLRP3. Finally, it suggests stabilizing the auto-inhibited form of the NACHT domain is an effective way to inhibit NLRP3, and will aid the structure-based development of NLRP3 inhibitors for a range of inflammatory diseases.