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| 1 | 3D-QSAR and Docking Studies of 1,3,4-Thiazolidinone Derivatives Using R-Group Search and Surflex-dock显示文摘In this paper, a three-dimensional quantitative structure-activity relationships(3 D-QSAR) study for 20 HIV-1 reverse transcriptase(RT) inhibitors was established using Topomer Co MFA. The models were built based on different fragment cutting models, with the most effective model of the multiple correlation coefficients of fitting(r^2) to be 0.920, cross-validation(q^2) of 0.575, and external validation(Q_(ext)~2) being 0.701. The results indicated that the model obtained has both favorable estimation stability and good prediction capability. Topomer Search was used to search R-group from ZINC database. As a result, a series of R-groups with relatively high activity contribution was obtained. By No. 6 molecule filtering, 3 R_1 and 15 R_2 groups were selected, and employed to alternately substitute for the R_1 and R_2 of sample 6. Finally, 45 new compounds were designed, and the Topomer CoMFA model was used to predicate the biological activity, so the Topomer Search is effective in screening and can guide the design of new HIV/AIDS drugs. The molecular docking method was also used to study the interactions of these drugs by docking the ligands into HIV-1 RT active site, which revealed the likely bioactive conformations. This study showed that there are extensive interactions between the 1,3,4-thiazolidinone revertase inhibitors and His84, Asp145, Lys33 and Leu83 residues in the active site of HIV-1 RT. These results provide useful insights for the design of potent new inhibitors of RT. | 仝建波 王洋 雷珊 秦尚尚 | 2019 | Chinese Journal of Structural Chemistry2019，38，3： | 19 |
| 2 | Anti-diabetic activity of quercetin extracted from Phyllanthus emblica L.fruit: In silico and in vivo approaches显示文摘In this study, molecular interactions of the ligands, quercetin, gallic acid, and metformin with various diabetes mellitus-related protein targets, such as glycogen phosphorylase and peroxisome proliferatoractivated receptor gamma, were assessed. It was revealed that quercetin possesses good binding affinity to both targets. Quercetin is a major constituent of methanolic extracts of Phyllanthus emblica fruit. The antihyperglycemic effect of quercetin in streptozotocin(STZ)-induced diabetic rats was examined. The isolated quercetin administered at a dose of 75 mg/kg body weight produced a maximum decrease of14.78% in blood glucose levels in the diabetic rats after 7 days of treatment. Furthermore, quercetin doses of 50 and 75 mg/kg were shown to significantly improve the profiles of triglycerides, high-density lipoprotein, very-low-density lipoprotein, low-density lipoprotein, and total cholesterol at the end of the study in STZ-induced diabetic rats. The administration of quercetin(25, 50, and 75 mg/kg body weight)daily for 28 days in STZ-induced diabetic rats resulted in a significant decrease in blood glucose and urine sugar levels, with a considerable rise in plasma insulin and hemoglobin levels. Therefore, quercetin is a potential drug with antidiabetic and antihyperglycemic action mediated by changes in the levels of glucose, cholesterol, and triglycerides as indicated by in silico and in vivo studies. | Prabhu Srinivasan S.Vijayakumar Swaminathan Kothandaraman Manogar Palani | 2018 | Journal of Pharmaceutical Analysis2018，8，2： | 18 |
| 3 | Computational network pharmacological research of Chinese medicinal plants for chronic kidney disease显示文摘The interaction between drug molecules and target proteins is the basis of pharmacological action.The pharmacodynamic mechanism of Chinese medicinal plants for chronic kidney disease(CKD) was studied by molecular docking and complex network analysis.It was found that the interaction network of components-proteins of Chinese medicinal plants is different from the interaction network of components-proteins of drugs.The action mechanism of Chinese medicinal plants is different from that of drugs.We also found the interaction network of components-proteins of tonifying herbs is different from the interaction network of components-proteins of evil expelling herbs using complex network research approach.It illuminates the ancient classification theory of Chinese medicinal plants.This computational approach could identify the pivotal components of Chinese medicinal plants and their key target proteins rapidly.The results provide data for development of multi-component Chinese medicine. | ZHU Wei1,QIU XiaoHui1,XU XiaoJie1,2* & LU ChuanJian1* 1Guangdong Hospital of Traditional Chinese Medicine,Guangzhou 510006,China 2College of Chemistry and Molecular Engineering,Peking University,Beijing 100871,China | 2010 | Science China Chemistry2010，53，11： | 13 |
| 4 | Computational pharmacological studies on cardiovascular disease by Qishen Yiqi Diwan显示文摘Computational pharmacological methods were used to study the distribution of 1729 compounds contained in a Chinese medicine,Qishen Yiqi Diwan,in chemical space.The results show that most of these compounds have good drug-like properties.Molecular docking was used to study the interactions between 1729 compounds of Qishen Yiqi Diwan and 26 drug targets related to cardiovascular disease and the distribution of 1729 compounds in drug-target space.The results may shed light on the action mechanism and the search for the active compounds in Qishen Yiqi Diwan. | GU JiangYong YUAN Gu ZHU YongHong XU XiaoJie | 2009 | Science China Chemistry2009，52，11： | 9 |
| 5 | A 3D-QSAR Study of HIV-1 Integrase Inhibitors Using RASMS and Topomer CoMFA显示文摘Acquired Immunodeficiency Syndrome(AIDS) is a significant human health threat around the world. Therefore, the study of anti-human immunodeficiency virus(HIV) drug design has become an important task for today’s society. In this paper, a three-dimensional quantitative structure-activity relationships study(3 D-QSAR) was conducted on 53 HIV-1 integrase inhibitors(IN) using random sampling analysis on molecular surface(RASMS) and Topomer comparative molecular field analysis(Topomer CoMFA). The multiple correlation coefficients of fitting, cross-validation, and external validation of two models were 0.926, 0.815 and 0.908 and 0.930, 0.726 and 0.855, respectively. The results indicated that two models obtained had both favorable estimation stability and good prediction capability. Topomer Search was used to search appropriate R groups from ZINC database, and 28 new compounds were designed thereby. The Topomer CoMFA model was subsequently used to predict the biological activity of these compounds, showing that 24 of the new compounds were more active than the template molecule. Ligands of the template molecule and new designed compounds were used for molecular docking to study the interaction of these compounds with the protein receptor. The results show that the ligands would form hydrogen-bonding interactions with the residues LEU58, THR83, GLN62, MET155, LYS119 and ALA154 of the protein receptor generally, thereby providing additional insights for the design of even more effective HIV/AIDS drugs. | 仝建波 秦尚尚 雷珊 王洋 | 2019 | Chinese Journal of Structural Chemistry2019，38，6： | 6 |
| 6 | Comprehensive 3D-QSAR and Binding Mode of DAPY Inhibitors Using R-group Search and Molecular Docking显示文摘The diarylpyrimidine(DAPY) compounds are important in the nonnucleoside reverse enzyme inhibitors. The present study is aimed at studying the three-dimensional quantitative structure-activity relationship(3D-QSAR) of DAPY inhibitors and their binding mode. We build a 3D-QSAR model involving 24 training DAPY inhibitors based on Topomer CoMFA, and 8 molecules are employed to validate the external predictive power of the model obtained. The multiple correlation coefficients of fitting, cross-validation and external validation were 0.979, 0.597 and 0.756, respectively. Topomer Search was employed as a tool for virtual screening in drug-like compounds of ZINC database(2012). Finally, we successfully design 30 new molecules with higher activity than that of all training and test inhibitors. The results indicated that Topomer CoMFA model had both favorable estimation stability and good predictive capability. Topomer Search technology could be effectively used to screen and design new compound, and had good predictive capability to guide the design of new Anti-HIV drugs. The molecular docking method was also used to study the interactions of these drugs by docking the ligands into HIV-1 reverse transcriptase active site, which revealed the likely bioactive conformations. This study showed extensive interactions between the DAPY derivatives and MET230, TRP229, PHE227, TYR318, TYR183, PRO95, GLY99, ILE100,TYR188, VAL106, TYR181, GLY190, GLU138, VAL179, THR139, ASN103 and LYS101 residues in the active site of HIV-1 reverse transcriptase. These results provide useful insights for the design of potent new inhibitors of HIV-1 reverse transcriptase. | 仝建波 王洋 雷珊 秦尚尚 | 2019 | Chinese Journal of Structural Chemistry2019，38，1： | 5 |
| 7 | Potential synergic mechanism of Wutou-Gancao herb-pair by inhibiting efflux transporter P-glycoprotein显示文摘Wutou-Gancao herb-pair is extensively used to attenuate the toxicity and enhance the efficacy of aconite.In this study,potential synergic mechanism of the herb pair was investigated by utilizing multiple ap-proaches.In silico and in vitro Caco-2 cell models were applied to study the potential binding mode of bioactive ingredients existing in liquorice with P-glycoprotein(P-gp),as well as the inhibition effects on P-gp.Additionally,anti-inflammatory activity of aconitine(AC)combined with active ingredients of liquorice,as well as pharmacokinetic patterns of AC after co-administration was investigated.Anti-inflammatory effect of AC(1 mg/kg)in rats was enhanced in combination with bioactive ingredients of liquorice(10 mg/kg).In the meanwhile,the exposure of AC in vivo was altered,in terms of Cmax and AUC.For instance,the Cmax and AUC were increased to 1.9 and 1.3 folds,respectively,when used in combination with liquiritigenin.The in silico study revealed the potential binding mode with outward facing conformation of P-gp.The resulting data obtained from transport of rhodamine-123(Rh-123)across Caco-2 cell monolayer further indicated that the function of P-gp was inhibited by chemicals in liquorice.The synergic effect was therefore proposed to be attributed to inhibition of P-gp by liquorice since AC has been demonstrated to be the substrate of P-gp.The resuls revealed that potential synergic mechanism of Wutou-Gancao herb-pair by inhibiting function of key efflux transporter P-gp to enhance the exposure of AC in systematic circulation,and further the anti-inflammatory effect,which helps clarify the compatibility rationale of these two herbs. | Yufei He Zihong Wei Ying Xie Xiulin Yi Yong Zeng Yazhuo Li Changxiao Liu | 2020 | Journal of Pharmaceutical Analysis2020，10，2： | 5 |
| 8 | Understanding the endocrine disruption of chiral pesticides:The enantioselectivity in estrogenic activity of synthetic pyrethroids显示文摘Synthetic pyrethroids(SPs) ,a family of chiral insecticides consisting of multiple stereoismers,have been regarded as estrogenic endocrine-disrupting chemicals(EDCs) .In this study,we applied the yeast two-hybrid and molecular docking(MD) assay to assess the enantioselective estrogenic activities of three commonly used SPs,bifenthrin(cis-BF) ,permethrin(PM) and fenvalerate(Fen) .The β-galactosidase analyses indicated that all of the testing pyrethroids displayed significant(p<0.05) enantioselectivity.The results showed that the estrogenic potential of cis-BF was mainly attributed to 1S-cis-BF.Neither PM nor Fen showed estrogenic effects.However,two stereoisomers of PM possessed estrogenic potential activities.αR-2R-Fen and αS-2S-Fen also induced the β-galactosidase activity.The inability to initiate the reporter gene expression by the racemic chemicals may be due to the low ratios of these isomers or the antagonism among them.The strong hydrophobic interaction and the hydrogen bond between positive estrogenic isomers and ERα support our biological testing results.This research demonstrated that the enantioselective estrogenic activity of chiral SPs was due to selective binding between their isomers and the ERαreceptor.The data suggests that enantioselectivity of these chiral pesticides is significant to their estrogenic activities. | WANG Cui 1,ZHANG Quan 1,ZHANG XiaoFeng 1,LIU Jing 2 & LIU WeiPing 2 1College of Biological and Environmental Engineering,Zhejiang University of Technology,Hangzhou 310032,China 2Key Laboratory of Environmental Remediation and Ecosystem Health,Ministry of Education College of Environmental and Resource Sciences,Zhejiang University,Hangzhou 310029,China | 2010 | Science China Chemistry2010，53，5： | 4 |
| 9 | Network pharmacology studies on the effect of Chai-Ling decoction incoronavirus disease 2019显示文摘Background:Chai-Ling decoction(CLD),derived from a modification of Xiao-Chai-Hu(XCH)decoction and Wu-Ling-San(WLS)decoction,has been used to treat the early-stage of coronavirus disease 2019(COVID-19).However,the mechanisms of CLD in COVID-19 remain unknown.In this study,the potential mechanisms of CLD in COVID-19 were preliminarily investigated based on network pharmacology and molecular docking method.Methods:Initially,the active components and targets of CLD were screened based on Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and PharmMapper database.The targets of COVID-19 were obtained from GeneCards database.The protein-protein interaction network was established using STRING database to analyze the key targets.Gene Oncology(GO)analysis and Kyoto Encyclopedia of Genes and Genomes analysis were also conducted to evaluate the pathways related to the targets of CLD on COVID-19.Moreover,the compound-target-pathway network was established using Cytoscape 3.2.7.Subsequently,the molecular docking method was performed to select the active compounds with high binding affinity on severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)and angiotensin-converting enzyme 2(ACE2),which is the key target of SARS-CoV-2 in entering target cells.The possible binding sites were also visualized by a three-dimensional graph.Results:Network pharmacology analysis showed that there were 106 active components and 160 targets of CLD.Additionally,251 targets related to COVID-19 were identified,and 24 candidates of CLD on COVID-19 were selected.A total of 283 GO terms of CLD on COVID-19 were identified,and 181 pathways were screened based on GO and Kyoto Encyclopedia of Genes and Genomes analyses.CLD might alleviate the inflammatory response and improve lung injury to treat COVID-19 through interleukin 17 signaling,T helper cell 17 differentiation,tumor necrosis factor signaling,and hypoxia inducible factor-1 signaling.Besides,molecular docking indicated that beta-sitosterol,kaempferol,and stigmasterol were the top three candidates in CLD with the highest affinity to SARS-CoV-2 and ACE2.Conclusion:Our study identifies the potential mechanisms of CLD on COVID-19 and beta-sitosterol,kaempferol,and stigmasterol may be the key compounds that exert antiviral effects against SARS-CoV-2. | Lu Yang Yu-Ting Li Jing Miao Li Wang Hui Fu Qin Li Wei-Bo Wen Zhai-Yi Zhang Rui-Wen Song Xiang-Guo Liu Hong-Wu Wang Huan-Tian Cui | 2020 | Traditional Medicine Research2020，5，3： | 4 |
| 10 | Structural insight into the serotonin (5-HT) receptor family by molecular docking, molecular dynamics simulation and systems pharmacology analysis显示文摘Serotonin (5-HT) receptors are proteins involved in various neurological and biological processes, such as aggression, anxiety, appetite, cognition, learning, memory, mood, sleep, and thermoregulation. They are commonly associated with drug abuse and addiction due to their importance as targets for various pharmaceutical and recreational drugs. However, due to a high sequence similarity/identity among 5-HT receptors and the unavailability of the 3D structure of the different 5-HT receptor, no report was available so far regarding the systematical comparison of the key and selective residues involved in the binding pocket, making it difficult to design subtype-selective serotonergic drugs. In this work, we first built and validated three-dimensional models for all 5- HT receptors based on the existing crystal structures of 5-HT1B, 5-HT2B, and 5-HT2C. Then, we performed molecular docking studies between 5-HT receptors agonists/inhibitors and our 3D models. The results from docking were consistent with the known binding affinities of each model. Sequentially, we compared the binding pose and selective residues among 5-HT receptors. Our results showed that the affinity variation could be potentially attributed to the selective residues located in the binding pockets. Moreover, we performed MD simulations for 12 5-HT receptors complexed with ligands;the results were consistent with our docking results and the reported data. Finally, we carried out off-target prediction and blood–brain barrier (BBB) prediction for Captagon using our established hallucinogen-related chemogenomics knowledgebase and in-house computational tools, with the hope to provide more information regarding the use of Captagon. We showed that 5-HT2C, 5-HT5A, and 5-HT7 were the most promising targets for Captagon before metabolism. Overall, our findings can provide insights into future drug discovery and design of medications with high specificity to the individual 5-HT receptor to decrease the risk of addiction and prevent drug abuse. | Yuan-qiang Wang Wei-wei Lin Nan Wu Si-yi Wang Mao-zi Chen Zhi-hua Lin Xiang-Qun Xie Zhi-wei Feng | 2019 | Acta Pharmacologica Sinica2019，40，9： | 4 |
| 11 | Progress in molecular docking显示文摘Background:In recent years,since the molecular docking technique can greatly improve the efficiency and reduce the research cost,it has become a key tool in computer-assisted drug design to predict the binding affinity and analyze the interactive mode.Results:This study introduces the key principles,procedures and the widely-used applications for molecular docking.Also,it compares the commonly used docking applications and recommends which research areas are suitable for them.Lastly,it briefly reviews the latest progress in molecular docking such as the integrated method and deep learning.Conclusion:Limited to the incomplete molecular structure and the shortcomings of the scoring function,current docking applications are not accurate enough to predict the binding affinity.However,we could improve the current molecular docking technique by integrating the big biological data into scoring function. | Jiyu Fan Ailing Fu Le Zhang | 2019 | Frontiers of Electrical and Electronic Engineering in China2019，7，2： | 3 |
| 12 | A Non-Redundant Benchmark for Symmetric Protein Docking显示文摘Symmetric proteins play important roles in many biological processes, such as signal transduction and molecular transportation. Therefore, determining the symmetric oligomeric structure of subunits is crucial to investigate the molecular mechanism of the related processes. Due to the high cost and technical difficulties associated with many experimental methods, computational approaches, such as molecular docking, have played an important complementary role in the determination of symmetric complex structures, in which a benchmark data set is pressingly needed. In the present work, we develop a comprehensive and non-redundant benchmark for symmetric protein docking based on the structures in the Protein Data Bank(PDB). The diverse dataset consists of 251 targets, including 212 cases with cyclic groups symmetry, 35 cases with dihedral groups symmetry, 3 cases with cubic groups symmetry, and 1 case with helical symmetry. According to the conformational changes in the interface between bound and unbound structures, the 251 targets were classified into three groups: 176 'easy',37 'medium', and 38 'difficult' cases. A preliminary docking test on the targets of cyclic groups symmetry with MZDOCK indicated that symmetric multimer docking remains challenging. The benchmark will be beneficial for the development of symmetric protein docking algorithms. The proposed benchmark data set is available for download at http://gffzz2d5067a24f40451dhx60bfqwc096c6nww.ffgz.tsg.suse.edu.cn/SDBenchmark/. | Yumeng Yan Sheng-You Huang | 2019 | Big Data Mining and Analytics2019，2，2： | 2 |
| 13 | Vitellaria paradoxa nutshells from seven sub-Saharan countries as potential herbal medicines for treating diabetes based on chemical compositions, HPLC fingerprints and bioactivity evaluation显示文摘The aim of the study was to determine the feasibility of the Vitellaria paradoxa nutshell as a new medicinal resource for treating diabetes. A total of forty-one compounds were identified by HPLC-DAD-Q-TOF-MS and phytochemical methods in V. paradoxa nutshell methanol extract. Based on HPLC fingerprints, four characteristic constituents were quantified and the origin of twenty-eight V. paradoxa nutshells from seven sub-Saharan countries was compared, which were classified into three groups with chemometric method. Twenty-eight samples contained high total phenolic content, and exhibited moderate-higher antioxidant activity and strong α-glucosidase inhibitory activity. Furthermore, all fractions and isolated compounds were evaluated for their antioxidant and α-glucosidase inhibitory activities, and α-glucosidase inhibitory action mechanism of four characteristic constituents including protocatechuic acid, 3, 5, 7-trihydroxycoumarin,(2 R, 3 R)-(+)-taxifolin and quercetin was investigated via molecular docking method, which were all stabilized by hydrogen bonds with α-glucosidase. The study provided an effective approach to waste utilization of V. paradoxa nutshell, which would help to resolve waste environmental pollution and provide a basis for developing potential herbal resource for treating diabetes. | LI Da XIAO Jian-Qi LIU Wen-Yuan ZHANG Chao-Feng AKIHISA Toshihiro ABE Masahiko MASTERS Eliot-T. ZHAI Wei-Wei FENG Feng ZHANG Jie | 2019 | Chinese Journal of Natural Medicines2019，17，6： | 2 |
| 14 | Combinatorial mutation on the β-glycosidase specific to 7-β-xylosyltaxanes and increasing the mutated enzyme production by engineering the recombinant yeast显示文摘Taxol is a 'blockbuster' antitumor drug produced by Taxus species with extremely low amount, while its analogue 7-β-xylosyl-10-deacetyltaxol is generally much higher in the plants. Both the fungal enzymes LXYL-P1à1 and LXYL-P1à2 can convert 7-β-xylosyl-10-deacetyltaxol into10-deacetyltaxol for Taxol semi-synthesis. Of them, LXYL-P1à2 is twice more active than LXYLP1à1, but there are only 11 significantly different amino acids in terms of the polarity and acidic-basic properties between them. In this study, single and multiple site-directed mutations at the 11 sites from LXYL-P1à1 to LXYL-P1à2 were performed to define the amino acids with upward bias in activities and to acquire variants with improved catalytic properties. Among all the 17 mutants, E12(A72 T/V91 S) was the most active and even displayed 2.8-and 3-fold higher than LXYL-P1à2 on β-xylosidase andβ-glucosidase activities. The possible mechanism for such improvement was proposed by homology modeling and molecular docking between E12 and 7-β-xylosyl-10-deacetyltaxol. The recombinant yeast GS115-P1 E12-7 was constructed by introducing variant E12, the molecular chaperone gene pdi and the bacterial hemoglobin gene vhb. This engineered yeast rendered 4 times higher biomass enzyme activity than GS115-3.5 K-P1à2 that had been used for demo-scale fermentation. Thus, GS115-P1 E12-7 becomes a promising candidate to replace GS115-3.5 K-P1à2 for industrial purpose. | Jing-Jing Chen Xiao Liang Fen Wang Yan-Hua Wen Tian-Jiao Chen Wan-Cang Liu Ting Gong Jin-Ling Yang Ping Zhu | 2019 | Acta Pharmaceutica Sinica B2019，9，3： | 2 |
| 15 | Interaction of repaglinide with bovine serum albumin:Spectroscopic and molecular docking approaches显示文摘Repaglinide (RPG) regulates the amount of glucose by stimulating the pancreas to release insulin in the blood. In view of its biological importance, we have examined the interaction between RPG and a model protein, bovine serum albumin (BSA) employing various spectroscopic, electrochemical and molecular docking methods. Fluorescence spectra of BSA were recorded in the presence and absence of RPG in phosphate buffer of pH 7.4. Fluorescence intensity of BSA was decreased upon the addition of increased concentrations of RPG, indicating the interaction between RPG and BSA. Stern-Volmer quenching analysis results revealed that RPG quenched the intensity of BSA through dynamic quenching mechanism. This was further confirmed from the time-resolved fluorescence measurements. The binding constant as calculated from the spectroscopic and voltammetric results was observed to be in the order of 104M-1 at 298 K, suggesting the moderate binding affinity between RPG and BSA. Competitive experimental results revealed that the primary binding site for RPG on BSA was site II. Absorption and circular dichroism studies indicated the changes in the secondary structure of BSA upon its interaction with RPG. Molecular simulation studies pointed out that RPG was bound to BSA in the hydrophobic pocket of site II. | Suma K.Pawar Seetharamappa Jaldappagari | 2019 | Journal of Pharmaceutical Analysis2019，9，4： | 2 |
| 16 | A holistic molecular docking approach for predicting protein-protein complex structure显示文摘A holistic protein-protein molecular docking approach,HoDock,was established,composed of such steps as binding site prediction,initial complex structure sampling,refined complex structure sampling,structure clustering,scoring and final structure selection.This article explains the detailed steps and applications for CAPRI Target 39.The CAPRI result showed that three predicted binding site residues,A191HIS,B512ARG and B531ARG,were correct,and there were five submitted structures with a high fraction of correct receptor-ligand interface residues,indicating that this docking approach may improve prediction accuracy for protein-protein complex structures. | GONG XinQi,LIU Bin,CHANG Shan,LI ChunHua,CHEN WeiZu & WANG CunXin* College of Life Science and Bioengineering,Beijing University of Technology,Beijing 100124,China | 2010 | Science China(Life Sciences)2010，53，9： | 2 |
| 17 | Study on the bioactivity changes of hydroxylated sulfonylureas derivatives: A possible metabolism显示文摘Some new sulfonylureas and their hydroxylation products had been synthesized from 2-amino-4-methylpyrimidine. Their bioactivities against E. coli AHAS II in vitro were tested and the results indicated that the hydroxylation decreased the inhibition activities of sulfonylureas significantly. Subsequently herbicidal tests against stem-growth of barnyard grass and root-growth of rape confirmed the above conclusion. The preliminary molecular docking studies were also carried out to investigate the binding modes of non-hydroxylated and hydroxylated sulfonylureas with AHAS. | Shu Rong Ban Cong Wei Niu Wen Bin Chen Zhi Hong Yu Si Wu Chen Wang Zhen Xi | 2007 | Chinese Chemical Letters2007，18，2： | 2 |
| 18 | Use of Network Pharmacology and Molecular Docking to Investigate the Mechanism by Which Ginseng Ameliorates Hypoxia显示文摘Hypoxia is a common pathological process in various clinical diseases and is characterized by abnormal changes in metabolism,function,and morphological structure of tissues resulting from insufficient oxygen supply or oxygen barriers in tissues.In particular,hypoxia in vital organs such as the brain and heart is an important cause of death[1].The prevention of tissue hypoxia and the treatment of hypoxia-induced tissue damage are urgent issues. | WANG Tao LI Hao Tian WEI Shi Zhang CAI Hua Dan ZHU Yun LIU Hong Hong LI Yong Zhi WANG Jia Ping ZOU Wen Jun ZHAO Yan Ling | 2018 | Biomedical and Environmental Sciences2018，31，11： | 2 |
| 19 | Fast docking of drug molecules to their receptor显示文摘AEDock based on AutoDock2.4 is developed with annealing evolution algorithm (AEA) in place of simulated annealing algorithm (SA) for supermolecular conformation searching. Because AEA takes advantage of both the genetic algorithm (GA) and the simulated annealing algorithm, the results of AEDock show that AEA can predict the binding conformations of ligands with up to 10 rotatable bonds to a rigid macromolecular target. The case of 1 hvr is only one of six cases where SA in AutoDock 2.4 failed to find an energy less than that of the crystal. It is used here to compare the performance of SA with AEA. The results of comparison show that fewer states are needed in AEA than in SA, but the success rate of AEA is much higher. | Jianquan Chen Hanlin Chi | 1999 | Chinese Science Bulletin1999，44，10： | 2 |
| 20 | Molecular modeling of the binding mode of chiral metal complexes A- and A-[Co(phen)_2dppz]^(3+) with B-DNA显示文摘Molecular modeling methods have been applied to the structural characterization of the interaction between chiral metal complexes [Co(phen)2dppz]3+ (where phen = 1, 10-phenanthroline, dppz = dipyrido[3,2-a: 2’, 3’-c]phenazine) and the oligonucleotide (B-DNA fragment). The natures of two kinds of the binding modes, which are currently intense controversy, have been explored. Barton proposed that there is enantio-selective DMA binding by the octahedral complexes and intercalative access by these complexes from the major groove; but Norden suggested that both enantiomers bind extremely strongly to DNA from the minor groove without any noticeable enantio-selectivity. Our results support and extend structural models based upon Norden’s studies, and conflict with Barton’s model. | 杨频 韩大雄 | 2000 | Science China Chemistry2000，43，5： | 2 |
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