2019
1 Chao Zhao,Dane Huang,Yida Xu,Shimin Su,Qiong Gu,and Jun Xu Identifying Novel Anti-Osteoporosis Leads with a Chemotype-Assembly Approach[J].Journal of Medicinal Chemistry, 2019 May 24 DOI PDF
1 Shuangjia Zheng,Xin Yan,Qiong Gu,Yuedong Yang,Yunfei Du,Yutong Lu and Jun Xu, QBMG: quasi-biogenic molecule generator with deep recurrent neural network[J]. Journal of Cheminformatics, 2019 January 17 DOI PDF
2018
1 Fang Y, Xia W, Cheng B, et al. Design, synthesis, and biological evaluation of compounds with a new scaffold as anti-neuroinflammatory agents for the treatment of Alzheimer's disease[J]. European journal of medicinal chemistry, 2018, 149: 129-138. DOI PDF
2 Zhihong Liu, Jiewen Du, Xin Yan, Jiali Zhong, Lu Cui, Jinyuan Lin, Lizhu Zeng, Peng Ding, pin chen, Xinxin Zhou, Huihao Zhou, Qiong Gu, and Jun Xu, TCMAnalyzer: a Chemo- and Bioinformatics Web Service for Analyzing Traditional Chinese Medicine, J. Chem. Inf. Model., 2018 Feb 8 DOI PDF
3 Xiang-Kun Luo†, Jie Cai†, Zhi-Yong Yin†, Pan Luo†, Chan-Juan Li†, Hang Ma‡, Navindra P. Seeram‡ , Qiong Gu*† , and Jun Xu†, Fluvirosaones A and B, Two Indolizidine Alkaloids with a Pentacyclic Skeleton from Flueggea virosa, Org. Lett., 2018 Jan 24 DOI PDF
4 Miao Yu, Qiong Gu, and Jun Xu*, Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening", Journal of Computer-Aided Molecular Design, 2018 Jan 6 DOI PDF
2017
1 Peng Ding, Xin Yan, Zhihong Liu, Jiewen Du, Yuehua Xu, Huihao Zhou, Qiong Gu, Jun Xu*, PTS: A Pharmaceutical Target Seeker, Database: The Journal of Biological Databases and Curation, 2017, 2017: bax095. Published online 2017 Dec 28 DOI PDF
2 Chanjuan Li, Bao Cheng, Sai Fang, Huihao Zhou, Qiong Gu, Jun Xu, Design, syntheses and lipid accumulation inhibitory activities of novel resveratrol mimics, European Journal of Medicinal Chemistry, Available online 7 November 2017, ISSN 0223-5234 DOI PDF
3 Yingchen Ju, Zhihong Liu, Zizhen Zhang, Lijun Duan, Qi Liu, Qiong Gu, Cheng Zhang, Jun Xu & Huihao Zhou, Membrane binding of the insertion sequence of Proteus vulgaris L-amino acid deaminase stabilizes protein structure and increases catalytic activity. Scientific Reports 7, Article number: 11121 (2017). DOI PDF
4 He Peng, Zhihong Liu, Xin Yan, Jian Ren & Jun Xu, A de novo substructure generation algorithm for identifying the privileged chemical fragments of liver X receptorβ agonists. Scientific Reports 7, Article number: 11121 (2017). DOI PDF
5 Jiali Zhong †, Zhihong Liu †, Xinxin Zhou * and Jun Xu *, Synergic Anti-Pruritus Mechanisms of Action for the Radix Sophorae Flavescentis and Fructus Cnidii Herbal Pair. Molecules 2017, 22(9), 1465. DOI PDF
6 Pan Luo, Qian Yu, Shao-Nan Liu, Wen-Juan Xia, Yu-Ying Fang, Lin-Kun An, Qiong Gu, Jun Xu, Diterpenoids with diverse scaffolds from Vitex trifolia as potential topoisomerase I inhibitor. In Fitoterapia, Volume 120, 2017, Pages 108-116, ISSN 0367-326X. DOI PDF
7 Pan Luo, Wenjuan Xia, Susan L. Morris-Natschke, Kuo-Hsiung Lee, Yu Zhao, Qiong Gu, and Jun Xu, Vitepyrroloids A−D, 2-Cyanopyrrole-Containing Labdane Diterpenoid Alkaloids from the Leaves of Vitex trifolia. J. Nat. Prod., 2017, 80 (5), pp 1679–1683. DOI PDF
8 Canrong Zhong , Mengyang Xu , Yan Wang, Jun Xu* , Yan Yuan*, An APE1 inhibitor reveals critical roles of the redox function of APE1 in KSHV replication and pathogenic phenotypes. PLoS Pathog, 2017 DOI PDF
9 Jie Cai, Chanjuan Li, Zhihong Liu, Jiewen Du, Jiming Ye, Qiong Gu, Jun Xu*. Predicting DPP-IV inhibitors with machine learning approaches. Journal of Computer-Aided Molecular Design, 2017: 1-10. DOI PDF
10 Yongsheng Lin†#, Qian Wang‡#, Qiong Gu*† , Hongao Zhang†, Cheng Jiang†, Jiayuan Hu‡, Yan Wang§, Yuan Yan*‡⊥, and Jun Xu*†. Semisynthesis of (−)-Rutamarin Derivatives and Their Inhibitory Activity on Epstein–Barr Virus Lytic Replication. J. Nat. Prod., 2017, 80 (1), pp 53–60 DOI PDF
2016
1 Jiewen Du, Xin Yan, Zhihong Liu, Lu Cui, Peng Ding, Xiaoqing Tan, Xiuming Li, Huihao Zhou, Qiong Gu* and Jun Xu*, cBinderDB: a covalent binding agent database, Bioinformatics, 2016 DOI PDF
2 Xiangkun Luo, Chanjuan Li, Pan Luo, Xin Lin, Hang Ma, Navindra P. Seeram, Ching Song, Jun Xu* , and Qiong Gu*, Pterosin Sesquiterpenoids from Pteris cretica as Hypolipidemic Agents via Activating Liver X Receptors, J. Nat. Prod., 2016, 79 (12), 3014–3021 DOI PDF
3 Shao-Nan Liu, Dane Huang, Susan L. Morris-Natschke, Hang Ma, Zhi-hong Liu, Navindra P. Seeram, Jun Xu, Kuo-Hsiung Lee, and Qiong Gu*. (2016). Euphomilones A and B, ent-Rosane Diterpenoids with 7/5/6 and 5/7/6 Skeletons from Euphorbia milii. Organic Letters, 18(23), 6132-6135. DOI PDF
4 Cheng Jiang, Pan Luo, Yu Zhao, Jialing Hong, Susan L. Morris-Natschke, Jun Xu, Chin-Ho Chen, Kuo-Hsiung Lee*, and Qiong Gu*. (2016). Carolignans from the aerial parts of Euphorbia sikkimensis and their anti-HIV activity. Journal of natural products, 79(3), 578-583. DOI PDF
5 Yingchen Ju, Shuilong Tong, Yongxiang Gao, Wei Zhao, Qi Liu, Qiong Gu, Jun Xu, Liwen Niub*, Maikun Tengb*, Huihao Zhoua*. (2016). Crystal structure of a membrane-bound L-amino acid deaminase from Proteus vulgaris. Journal of Structural Biology, 195(3), 306-315. DOI PDF
6 Liu, Z.; Ding, P.; Yan, X.; Zheng, M.; Zhou, H.; Xu, Y.; Du, Y.; Gu, Q.; Xu, J., ASDB: a resource for probing protein functions with small molecules. Bioinformatics 2016 DOI PDF
7 Wang, L.; Chen, L.; Yu, M.; Xu, L. H.; Cheng, B.; Lin, Y. S.; Gu, Q.; He, X. H.; Xu, J., Discovering new mTOR inhibitors for cancer treatment through virtual screening methods and in vitro assays. Sci. Rep. 2016, 6 DOI PDF
2015
1 Gongrui Guo, Yongxiang Gao, Zhongliang Zhu, Debiao Zhao, Zhihong Liu, Huihao Zhou*, Liwen Niu*, Maikun Teng*. (2015). Structural and biochemical insights into the DNA-binding mode of MjSpt4p: Spt5 complex at the exit tunnel of RNAPII. Journal of structural biology, 192(3), 418-425. DOI PDF
2 Li, L.; Le, X.; Wang, L.; Gu, Q.; Zhou, H. H.; Xu, J., Discovering new DNA gyrase inhibitors using machine learning approaches. Rsc Adv 2015, 5:105600-105608 DOI PDF
3 Yan, X.; Liao, C.; Liu, Z.; Hagler, A. T.; Gu, Q.; Xu, J., Chemical Structure Similarity Search for Ligand-Based Virtual Screening: Methods and Computational Resources. Curr Drug Targets 2015. DOI PDF
4 Cui, L.; Wang, Y.; Liu, Z.; Chen, H.; Wang, H.; Zhou, X.; Xu, J., Discovering New Acetylcholinesterase Inhibitors by Mining the Buzhongyiqi Decoction Recipe Data. J Chem Inf Model 2015, 55, 2455-2463. DOI PDF
5 Qianzhi Ding, Chanjuan Li,Ling Wang,Yali Li, Huihao Zhou,Qiong GuandJun Xu,Identifying farnesoid X receptor agonists by naïve Bayesian and recursive partitioning approaches . Med. Chem. Commun.2015,6, 1393-1403 DOI PDF
6 Xiu Le,Qiong Gu and Jun Xu., Identifying MurI uncompetitive inhibitors by correlating decomposed binding energies with bioactivity . RSC Adv.2015,5, 40536-40545 DOI PDF
7 Wu, T.; Wang, Q.; Jiang, C.; Morris-Natschke, S. L.; Cui, H.; Wang, Y.; Yan, Y.; Xu, J.; Lee, K. H.; Gu, Q., Neo-clerodane diterpenoids from Scutellaria barbata with activity against Epstein-Barr virus lytic replication. Journal of Natural Products 2015, 78, 500-509 DOI PDF
8 Li, Y.; Wang, L.; Liu, Z.; Li, C.; Xu, J.; Gu, Q.; Xu, J., Predicting selective liver X receptor beta agonists using multiple machine learning methods. Mol Biosyst 2015, 11, 1241-1250 DOI PDF
9 Sai Fang, L. C., Miao Yu, Bao Cheng, Yongsheng Lin, Susan L. Morris-Natschke, Kuo-Hsiung Lee, Qiong Gu and Jun Xu, Synthesis, Antitumor Activity, and Mechanism of Action of 6-Acrylic Phenethyl Ester-2-pyranone Derivatives. Organic & biomolecular chemistry 2015 DOI PDF
10 Yan X, D. P., Liu Z H, Wang, L., Liao C, Gu, Q. and Xu, J, Big data in drug design. Chin Sci Bull 2015, 60, 558-565 DOI PDF
2014
1 Wang, L.; Le, X.; Li, L.; Ju, Y.; Lin, Z.; Gu, Q.; Xu, J., Discovering New Agents Active against Methicillin-Resistant Staphylococcus aureus with Ligand-Based Approaches. Journal of chemical information and modeling 2017, 54, (11), 3186-97. DOI PDF
2 Li, C.; Ge, H.; Cui, L.; Li, Y.; Cheng, B.; Zhang, G.; Zhang, Z.; Qi, H.; Ruan, Y.; Gu, Q.; Xu, J., Molecular mechanism of action of K(D)PT as an IL-1RI antagonist for the treatment of rhinitis. RSC Adv. 2017, 4, 48741-48749 DOI PDF
3 Wang, Y.; Ge, H.; Li, Y.; Xie, Y.; He, Y.; Xu, M.; Gu, Q.; Xu, J., Predicting dual-targeting anti-influenza agents using multi-models. Molecular Diversity 2017. DOI PDF
4 Chen, L.; Wang, L.; Gu, Q.; Xu, J., An in silico protocol for identifying mTOR inhibitors from natural products. Molecular Diversity 2017, 18, (4), 841-52 DOI PDF
5 Liu, Z.; Zhou, J.; Wu, R.; Xu, J., Mechanism of Assembling Isoprenoid Building Blocks 1. Elucidation of the Structural Motifs for Substrate Binding in Geranyl Pyrophosphate Synthase. Journal of Chemical Theory and Computation 2017, 10, (11), 5057-5067. DOI PDF
6 Zheng, M.; Liu, Z.; Yan, X.; Ding, Q.; Gu, Q.; Xu, J., LBVS: an online platform for ligand-based virtual screening using publicly accessible databases. Molecular Diversity 2017, 18, (4), 829-40. DOI PDF
7 Shu, C.; Ge, H.; Song, M.; Chen, J. H.; Zhou, H.; Qi, Q.; Wang, F.; Ma, X.; Yang, X.; Zhang, G.; Ding, Y.; Zhou, D.; Peng, P.; Shih, C. K.; Xu, J.; Wu, F., Discovery of Imigliptin, a Novel Selective DPP-4 Inhibitor for the Treatment of Type 2 Diabetes. ACS medicinal chemistry letters 2017, 5, (8), 921-6. DOI PDF
8 Zhou, J.; Xie, H.; Liu, Z.; Luo, H. B.; Wu, R., Structure-Function Analysis of the Conserved Tyrosine and Diverse pi-Stacking among Class I Histone Deacetylases: A QM (DFT)/MM MD Study. Journal of Chemical Information and Modeling 2017, 54, (11), 3162-71. DOI PDF
9 Ge, H.; Liu, J. G.; Zhao, W. X.; Wang, Y.; He, Q. Q.; Wu, R. B.; Li, D.; Xu, J., Mechanistic studies for tri-targeted inhibition of enzymes involved in cholesterol biosynthesis by green tea polyphenols. Organic & biomolecular chemistry 2017, 12, (27), 4941-4951 DOI PDF
10 Ge, H.; Wang, Y.; Zhao, W. X.; Lin, W.; Yan, X.; Xu, J., Scaffold hopping of potential anti-tumor agents by WEGA: a shape-based approach. Medchemcomm 2017, 5, (6), 737-741 DOI PDF
11 Cui, H.; Xu, B.; Wu, T.; Xu, J.; Yuan, Y.; Gu, Q., Potential antiviral lignans from the roots of Saururus chinensis with activity against Epstein-Barr virus lytic replication. Journal of Natural Products 2017, 77, (1), 100-10. DOI PDF
12 Ge, H.; Liu, G.; Xiang, Y. F.; Wang, Y.; Guo, C. W.; Chen, N. H.; Zhang, Y. J.; Wang, Y. F.; Kitazato, K.; Xu, J., The mechanism of poly-galloyl-glucoses preventing Influenza A virus entry into host cells. PloS one 2017, 9, (4), e94392. DOI PDF
13 Liu, Z.; Zheng, M.; Yan, X.; Gu, Q.; Gasteiger, J.; Tijhuis, J.; Maas, P.; Li, J.; Xu, J., ChemStable: a web server for rule-embedded naive Bayesian learning approach to predict compound stability. Journal of Computer-aided Molecular Design 2017, 28, (9), 941-50. DOI PDF
14 Wang, L.; Chen, L.; Liu, Z.; Zheng, M.; Gu, Q.; Xu, J., Predicting mTOR inhibitors with a classifier using recursive partitioning and Naive Bayesian approaches. PloS one 2017, 9, (5), e95221. DOI PDF
15 Wu, T. Z.; Cui, H.; Cheng, B.; Fang, S.; Xu, J.; Gu, Q., Chemical constituents from the roots of Elephantopus scaber L. Biochem Syst Ecol 2017, 54, 65-67. DOI PDF
16 Xu, B.; Wang, L.; Gonzalez-Molleda, L.; Wang, Y.; Xu, J.; Yuan, Y., Antiviral activity of (+)-rutamarin against Kaposi's sarcoma-associated herpesvirus by inhibition of the catalytic activity of human topoisomerase II. Antimicrobial agents and chemotherapy 2017, 58, (1), 563-73. DOI PDF
17 Yan, X.; Li, J.; Gu, Q.; Xu, J., gWEGA: GPU-accelerated WEGA for molecular superposition and shape comparison. Journal of Computational Chemistry 2017, 35, (15), 1122-30. DOI PDF
18 Zhang, W.; Wang, L.; Zhang, L.; Chen, W.; Chen, X.; Xie, M.; Yan, G.; Hu, X.; Xu, J.; Zhang, J., Synthesis and biological evaluation of steroidal derivatives as selective inhibitors of AKR1B10. Steroids 2017, 86, 39-44. DOI PDF
19 Cao, Y.; Wang, L.; Lin, Z.; Liang, F.; Pei, Z.; Xu, J.; Gu, Q., Dehydroabietylamine derivatives as multifunctional agents for the treatment of Alzheimer's disease. Medchemcomm 2017, 5, (11), 1736-1743. DOI PDF
20 Chen, N. H.; Zhou, J. W.; Li, J. B.; Xu, J.; Wu, R. B., Concerted Cyclization of Lanosterol C-Ring and D-Ring Under Human Oxidosqualene Cyclase Catalysis: An ab Initio QM/MM MD Study. Journal Of Chemical Theory And Computation 2017, 10, (3), 1109-1120 DOI PDF
2013
1 Cao, Y. Y.; Wang, L.; Ge, H.; Lu, X. L.; Pei, Z.; Gu, Q.; Xu, J., Salvianolic acid A, a polyphenolic derivative from Salvia miltiorrhiza bunge, as a multifunctional agent for the treatment of Alzheimer's disease. Molecular Diversity 2013, 17, (3), 515-24. DOI PDF
2 Dong, Y. N.; Wang, L.; Gu, Q.; Chen, H.; Liu, X.; Song, Y.; Chen, W.; Hagler, A. T.; Zhang, H.; Xu, J., Optimizing lactose hydrolysis by computer-guided modification of the catalytic site of a wild-type enzyme. Molecular Diversity 2013, 17, (2), 371-82. DOI PDF
3 Ge, H.; Wang, Y.; Li, C.; Chen, N.; Xie, Y.; Xu, M.; He, Y.; Gu, X.; Wu, R.; Gu, Q.; Zeng, L.; Xu, J., Molecular dynamics-based virtual screening: accelerating the drug discovery process by high-performance computing. Journal of Chemical Information and Modeling 2013, 53, (10), 2757-64. DOI PDF
4 Gu, Q.; Chen, Y. Y.; Cui, H.; Huang, D. N.; Zhou, J. W.; Wu, T. Z.; Chen, Y. P.; Shi, L. N.; Xu, J., Chrysanolide A, an unprecedented sesquiterpenoid trimer from the flowers of Chrysanthemum indicum L. Rsc Adv 2013, 3, (26), 10168-10172. DOI PDF
5 Gu, Q.; Yan, X.; Xu, J., Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome. J Pharm Pharm Sci 2013, 16, (2), 331-341 DOI PDF
6 Wang, L.; Gu, Q.; Zheng, X.; Ye, J.; Liu, Z.; Li, J.; Hu, X.; Hagler, A.; Xu, J., Discovery of new selective human aldose reductase inhibitors through virtual screening multiple binding pocket conformations. Journal of Chemical Information and Modeling 2013, 53, (9), 2409-22. DOI PDF
7 Xu, J.; Gu, Q.; Liu, H. B.; Zhou, J. J.; Bu, X. Z.; Huang, Z. S.; Lu, G.; Li, D.; Wei, D. Q.; Wang, L.; Gu, L. Q., Chemomics and drug innovation. Sci China Chem 2013, 56, (1), 71-85. DOI PDF
8 Yan, X.; Li, J.; Liu, Z.; Zheng, M.; Ge, H.; Xu, J., Enhancing molecular shape comparison by weighted Gaussian functions. Journal of Chemical Information and Modeling 2013, 53, (8), 1967-78. DOI PDF
9 Zhang, G. D.; Ge, H.; Gu, Q.; Xu, J., Predicting hiCE inhibitors based upon pharmacophore models derived from the receptor and its ligands. Sci China Chem 2013, 56, (10), 1402-1412. DOI PDF
2012
1 Huang, D.; Gu, Q.; Ge, H.; Ye, J.; Salam, N. K.; Hagler, A.; Chen, H.; Xu, J., On the value of homology models for virtual screening: discovering hCXCR3 antagonists by pharmacophore-based and structure-based approaches. Journal of Chemical Information and Modeling 2012, 52, (5), 1356-66. DOI PDF
2 Lu, F.; Gu, Q.; Wu, R.; Xu, J., A structure-similarity-based software for the cardiovascular toxicity prediction of traditional chinese medicine. Bioinformation 2012, 8, (2), 110-3 DOI PDF
3 Wu, R.; Gong, W.; Liu, T.; Zhang, Y.; Cao, Z., QM/MM molecular dynamics study of purine-specific nucleoside hydrolase. The Journal of Physical Chemistry. B 2012, 116, (6), 1984-91. DOI PDF
4 Xu, J.; Xu, J.; Chen, H., Interpreting the structural mechanism of action for MT7 and human muscarinic acetylcholine receptor 1 complex by modeling protein-protein interaction. Journal of biomolecular structure & dynamics 2012, 30, (1), 30-44. DOI PDF
5 Yan, X.; Gu, Q.; Lu, F.; Li, J.; Xu, J., GSA: a GPU-accelerated structure similarity algorithm and its application in progressive virtual screening. Molecular Diversity 2012, 16, (4), 759-69. DOI PDF
6 Zeng, X. Y.; Zhou, X.; Xu, J.; Chan, S. M.; Xue, C. L.; Molero, J. C.; Ye, J. M., Screening for the efficacy on lipid accumulation in 3T3-L1 cells is an effective tool for the identification of new anti-diabetic compounds. Biochemical pharmacology 2012, 84, (6), 830-7. DOI PDF
2011
1 Fang, J.; Huang, D.; Zhao, W.; Ge, H.; Luo, H. B.; Xu, J., A new protocol for predicting novel GSK-3beta ATP competitive inhibitors. Journal of Chemical Information and Modeling 2011, 51, (6), 1431-8. DOI PDF
2 Hou, J.; Xu, J.; Liu, M.; Zhao, R.; Luo, H. B.; Ke, H., Structural asymmetry of phosphodiesterase-9, potential protonation of a glutamic acid, and role of the invariant glutamine. PloS one 2011, 6, (3), e18092. DOI PDF
3 Liu, H.; Ge, H.; Peng, Y.; Xiao, P.; Xu, J., Molecular mechanism of action for reversible P2Y12 antagonists. Biophysical Chemistry 2011, 155, (2-3), 74-81. DOI PDF
4 Yan, A.; Wang, L.; Xu, S.; Xu, J., Aurora-A kinase inhibitor scaffolds and binding modes. Drug Discovery Today 2011, 16, (5-6), 260-9. DOI PDF
5 Zhao, W.; Gu, Q.; Wang, L.; Ge, H.; Li, J.; Xu, J., Three-dimensional pharmacophore modeling of liver-X receptor agonists. Journal of Chemical Information and Modeling 2011, 51, (9), 2147-55. DOI PDF
2010
1 Ge, H.; Wang, Y. F.; Xu, J.; Gu, Q.; Liu, H. B.; Xiao, P. G.; Zhou, J. J.; Liu, Y. H.; Yang, Z. R.; Su, H., Anti-influenza agents from Traditional Chinese Medicine. Nat Prod Rep 2010, 27, (12), 1758-1780 DOI PDF
2 Ding, X.; Jiang, L.; Ke, C.; Yang, Z.; Lei, C.; Cao, K.; Xu, J.; Xu, L.; Yang, X.; Zhang, Y.; Huang, P.; Huang, W.; Zhu, X.; He, Z.; Liu, L.; Li, J.; Yuan, J.; Wu, J.; Tang, X.; Li, M., Amino acid sequence analysis and identification of mutations under positive selection in hemagglutinin of 2009 influenza A (H1N1) isolates. Virus Genes 2010, 41, (3), 329-40. DOI PDF
3 Gu, Q.; Xu, J.; Gu, L., Selecting diversified compounds to build a tangible library for biological and biochemical assays. Molecules 2010, 15, (7), 5031-44. DOI PDF
4 Liu, H. B.; Cui, W.; Xu, J.; Peng, Y.; Zhou, J. J.; Xiao, P. G., Molecular Simulations of the Inhibition of Active Components in Traditional Chinese Medicine on the Thromboxane A2 Receptor. Acta Phys-Chim Sin 2010, 26, (9), 2549-2556. DOI PDF
5 Liu, H. B.; Xu, J.; Peng, Y.; Zhou, J. J.; Xiao, P. G., Targets of Danshen's Active Components for Activating Blood Circulation Activities. Acta Phys-Chim Sin 2010, 26, (1), 199-205. DOI PDF