Molecular Modeling & Drug Design

Medicinal Chemistry

Drug Design
Molecular Modeling & Drug Design
Analytical Chemistry
Physical Chemistry

1. Guimin Wang, Weiliang Zhu*, Molecular docking for drug discovery and development: a widely used approach but far from perfect, Future Medicinal Chemistry, 2016, 8(14), 1707-1710.

2. Zhaoqiang Chen¹, Guimin Wang¹, Zhijian Xu^*, Jinan Wang, Yuqi Yu, Tingting Cai, Qiang Shao, Jiye Shi^*, and Weiliang Zhu^*, How do Distance and Solvent Affect the Halogen Bonding Involving Negatively Charged Donors? J. Phys. Chem. B 2016, 120 (34), 8784-8793.

3. Yisu Li¹, Binbin Guo¹, Zhijian Xu^*, Bo Li, Tingting Cai, Xinben Zhang, Yuqi Yu, Heyao Wang^*, Jiye Shi, Weiliang Zhu^*, Repositioning organohalogen drugs: a case study for identification of potent B-Raf V600E inhibitors via docking and bioassay. Scientific Reports 2016, 6, 31074.

4. Xia Liu¹, Zhijian Xu¹, Chuanwei Hou¹, Meng Wang, Xinhuan Chen, Qinghui Lin, Rui Song,Meng Lou, Lijun Zhu, Yunqing Qiu, Zhi Chen, Chunhao Yang^*, Weiliang Zhu^*, Jimin Shao^*, Inhibition of hepatitis B virus replication by targeting ribonucleotide reductase M2 protein. Biochem. Pharmacol. 2016, 103, 118-128.

5. Jinan Wang, Qiang Shao^*, Benjamin P. Cossins, Jiye Shi^*, Kaixian Chen & Weiliang Zhu^*,Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters. J Biomol Struct Dyn.2016,34,163-176.

6. Yuqi Yu, Jinan Wang, Qiang Shao^*, Jiye Shi^*, Weiliang Zhu^*. The effects of organic solvents on the folding pathway and associated thermodynamics of proteins: A microscopic view. Sci. Rep. 2016, 6,19500.

7. Yunfei Zhou, Jianming Zhu, Bo Li,* Yong Zhang, Jia Feng, Adrian Hall, Jiye Shi,* Weiliang Zhu*. Access to Different Isomeric Dibenzoxazepinones through Copper-Catalyzed C-H Etherification and C-N Bond Construction with Controllable Smiles Rearrangement, Org Lett. 2016, 18, 380-383.

8. Jianming Zhu¹, Xiaolong Li¹, Guimin Wang, Bo Li,* Zhijian Xu, Shikai Tian, Adrian Hall, Jingshan Shen, Jiye Shi,* Weiliang Zhu*. Facile Synthesis of Substituted 4-Alkoxy-2-oxazolines and Exploration of the Reaction Mechanism, Synthesis 2016, 48, 1331-1343.

9. Guimin Wang, Zhaoqiang Chen, Zhijian Xu*, Jinan Wang, Yang Yang, Tingting Cai, Jiye Shi*, Weiliang Zhu*, Stability and Characteristic of the Halogen Bonding Interaction in Anion-Anion Complex: A Computational Chemistry Study, J. Phys. Chem. B, 2016, 120(4):610-20.

10. Yang Yang, Zhijian Xu*, Zhengyan Zhang, Zhuo Yang, Yingtao Liu, Jinan Wang, Tingting Cai, Shujin Li, Kaixian Chen, Jiye Shi*, Weiliang Zhu*, Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design? J. Phys. Chem. B 2015, 119(36), 11988-11997.

11. Yuqi Yu, Jinan Wang, Qiang Shao*, Jiye Shi*, Weiliang Zhu*,·Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir. Scientific Reports,2015,5,10517

12. Yuqi Yu,¹ Jinan Wang,¹ Qiang Shao*, Jiye Shi*, Weiliang Zhu*, Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation. J. Chem. Phys. 2015, 142(12),125105

13. Jinan Wang, Qiang Shao*, Benjamin P Cossins, Jiye Shi*, Kaixian Chen, Weiliang Zhu*, Thermodynamics calculation of protein–ligand interactions by QM/MM polarizable charge parameters. Journal of biomolecular Structure & Dynamics 2015; DOI:10.1080/07391102.2015.1019928

14. Zhuo Yang¹, Yingtao Liu¹, Zhaoqiang Chen, Zhijian Xu*, Jiye Shi*, Kaixian Chen, Weiliang Zhu*, A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions. Journal of molecular modeling 2015, 21 (6), 1-21.

15. Xiuming Xiong, Zhaoqiang Chen, Benjamin P. Cossins, Zhijian Xu, Qiang Shao, Kai Ding, Weiliang Zhu*, Jiye Shi*, Force fields and scoring functions for carbohydrate simulation, Carbohydrate Research, 2015, 401, 73–81

16. Bing Zhou,* Zhaoqiang Chen, Yaxi Yang,* Wen Ai, Huanyu Tang, Yunxiang Wu, Weiliang Zhu,* and Yuanchao Li, Redox-Neutral Rhodium-Catalyzed C[BOND]H Functionalization of Arylamine N-Oxides with Diazo Compounds: Primary C(sp3)[BOND] H/C(sp2)[BOND]H Activation and Oxygen-Atom Transfer, Angew. Chem. Int. Ed., 2015 , 41, 12121-12126

17. Meining Wang,‡ Yang Yang,‡ Zhoulong Fan, Zhen Cheng,* Weiliang Zhu* and Ao Zhang*, Pd-catalyzed a-selective C(sp3)–H acetoxylation of amides through an unusual cyclopalladation mechanism, ChemComm, 2015,  51, 3219--3222

18. Tao Jiang,† Yuren Zhou,† Zhuxi Chen,† Peng Sun, Jianming Zhu, Qiang Zhang, Zhen Wang, Qiang Shao, Xiangrui Jiang,* Bo Li,* Kaixian Chen, Hualiang Jiang, Heyao Wang,* Weiliang Zhu, and Jingshan Shen. Design, Synthesis, and Pharmacological Evaluation of Fused β‑Homophenylalanine Derivatives as Potent DPP‑4 Inhibitors. ACS Med. Chem. Lett. 2015, 6, 602−606

19. Tao Jiang, † Yuren Zhou, † Jianming Zhu, † Zhuxi Chen, Peng Sun, Qiang Zhang, Zhen Wang, Qiang Shao, Xiangrui Jiang*, Bo Li*, Heyao Wang*, Weiliang Zhu, and Jingshan Shen. Design, Synthesis, and Pharmacological Evaluation of Highly Potent and Selective Dipeptidyl Peptidase-4 Inhibitors. Arch. Pharm. Chem. Life Sci. 2015, 348, 1–9

20. Guoxin Du, Li Feng, Zhuo Yang, Jiye Shi, Cheng Huang, Fujiang Guo, Bo Li, Weiliang Zhu,* Yiming Li*. Separation and peroxisome proliferator-activated receptor-c agonist activity evaluation of synthetic racemic bavachinin enantiomers. Bioorg. Med. Chem. Lett. 2015, 25, 2579–2583

21. Zhuo  Yang¹, Zhijian  Xu¹, Yingtao  Liu, Jinan  Wang, Jiye  Shi*, Kaixian  Chen, and  Weiliang  Zhu*, Unstable, Metastable, or Stable Halogen Bonding Interaction Involving Negatively Charged Donors? A Statistical and Computational Chemistry Study, J. Phys. Chem. B 2014, 118, 14223−14233

22. Xinhuan Chen¹, Zhijian Xu¹, Lingna Zhang, Hongchuan Liu,Xia Liu, Meng Lou, Lijun Zhu, Bingding Huang, CaiGuang Yang, Weiliang Zhu*, and Jimin Shao*, The conserved Lys-95 charged residue cluster is critical for the homodimerization and enzyme activity of human ribonucleotide reductase small subunit M2. J. Biol. Chem. 2014, 289(2), 909-920,

23. Jinan Wang, Shaoliang Peng, Benjamin P. Cossins,Xiangke Liao, Kaixian Chen, Qiang Shao,*Xiaoqian Zhu,*Jiye Shi*, and Weiliang Zhu. Mapping Central α-Helix Linker Mediated Conformational Transition Pathway of Calmodulin via Simple Computational Approach. J. Phys. Chem. B ,2014, 118, 9677−9685

24. ZHANG Yong, GAO Yuan-yuan, JIA Qi, GUO Fu-jiang, LI Bo, XU Zhi-jian,LI Yi-ming*, ZHU Wei-liang*, CHEN Kai-xian，Two new sulfated sesquiterpenoids from Petasites tricholobus. Acta Pharmaceutica Sinica, 2014, 49 (10): 1433 −1437

25. Zhijian Xu, Zhuo Yang, Yingtao Liu, Yunxiang Lu, Kaixian Chen, Weiliang Zhu, Halogen Bond: Its Role beyond Drug–Target Binding Affinity for Drug Discovery and Development, J. Chem. Inf. Model., 2014, 54, 69–78

26. Jinan Wang, Qiang Shao, Zhijian Xu, Yingtao Liu, Zhuo Yang, Benjamin P. Cossins, Hualiang Jiang, Kaixian Chen, Jiye Shi, Weiliang Zhu, Exploring Transition Pathway and Free-Energy Profile of Large-Scale Protein Conformational Change by Combining Normal Mode Analysis and Umbrella Sampling Molecular Dynamics, J. Phys. Chem. B, 2014, 118, 134–143

27. Bo Li, Gaihong Wang, Zhijian Xu, Yong Zhang, Xiangui Huang, Bubing Zeng, Kaixian Chen, Jiye Shi, Heyao Wang, Weiliang Zhu, Discovery of N-substituted 3-arylisoquinolone derivatives as antitumor agents originating from O-substituted 3-arylisoquinolines via [2,3] or [3,3] rearrangement, European Journal of Medicinal Chemistry, 2014, 77, 204–210

28. Ying-tao LIU, Yi LI, Zi-fu HUANG1, Zhi-jian XU, Zhuo YANG, Zhu-xi CHEN, Kai-xian CHEN, Ji-ye SHI, Wei-liang ZHU, Multi-algorithm and multi-model based drug target prediction and web server, Acta Pharmacologica Sinica, 2014, 35, 419–431

29. ZENG Peng, ZHANG Yong, PAN Chen, JIA Qi, GUO Fu-jiang, ZHU Wei-liang, LI Yi-ming, CHEN Kai-xian, Phenolic constituents from Lysimachia patungensis, Acta Pharmaceutica Sinica, 2013, 48(3), 377-382

30. Bo Li, Gaihong Wang, Mu Yang, Zhijian Xu, Bubing Zeng, Heyao Wang, Jingshan Shen, Kaixian Chen, Weiliang Zhu, Overman rearrangement and PomeranzeFritsch reaction for the synthesis of benzoazepinoisoquinolones to discover novel antitumor agents,European Journal of Medicinal Chemistry, 2013, 70, 677-684

31. Yingtao Liu, Zhijian Xu, Zhuo Yang, Kaixian Chen, Weiliang Zhu, A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions, J Mol Model, 2013, 19, 5015-5030

32. Enguang Feng, Woo-Jin Shin,Xuelian Zhu, Jian Li,Deju Ye, Jiang Wang,Mingyue Zheng,Jian-Ping Zuo, Kyoung Tai No, Xian Liu, Weiliang Zhu,*Wei Tang,* Baik-Lin Seong,*Hualiang Jiang, and Hong Liu*Structure-based design and synthesis of C-1- and C-4-modified analogs of zanamivir as neuraminidase inhibitors. J Med Chem. 2013, 56(3),671-84.

33. Jinan Wang, Tim Fulford, Qiang Shao, Arnaud Javelle, Huaiyu Yang, Weiliang Zhu*,Mike Merrick*.Ammonium transport proteins with changes in one of the conserved pore histidines have different performance in ammonia and methylamine conduction. PLoS One. 2013,8(5),e62745

34. Zhengyan Zhang, Zhijian Xu, Zhuo Yang, Yingtao Liu,Jin’an Wang,Qiang Shao, Shujin Li,* Yunxiang Lu,* and Weiliang Zhu*.The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: database survey and computational studies. J Phys Chem B. 2013,117(17),4827-35.

35. Xiuming Xiong, Zhijian Xu, Zhuo Yang, Yingtao Liu, Di Wang, Mei Dong, Emily J. Parker,* Weiliang Zhu*. Key targets and relevant inhibitors for the drug discovery of tuberculosis. Curr Drug Targets. 2013,14(6),676-99

36. Peng Sun, Ting Wang, Yuren Zhou, Hong Liu, Hualiang Jiang, Weiliang Zhu*, Heyao Wang* DC260126: a small-molecule antagonist of GPR40 that protects against pancreatic β-Cells dysfunction in db/db mice. PLoS One. 2013 ,8(6),e66744

37. Di Wang, Xuelian Zhu, Changjun Cui, Mei Dong, Hualiang Jiang, Zhengming Li, Zhen Liu,*Weiliang Zhu,* and Jian-Guo Wang*.Discovery of novel acetohydroxyacid synthase inhibitors as active agents against Mycobacterium tuberculosis by virtual screening and bioassay. J Chem Inf Model. 2013 ,53(2),343-53

38. Jing Deng, Ning Li, Hongchuan Liu, Zhili Zuo, Oi Wah Liew, Weijun Xu, Gang Chen, Xiankun Tong, Wei Tang*, Jin Zhu, Jianping Zuo, Hualiang Jiang, Cai-Guang Yang*, Jian Li*, Weiliang Zhu*, Discovery of Novel Small Molecule Inhibitors of Dengue Viral NS2BNS3 Protease Using Virtual Screening and Scaffold Hopping, J. Med. Chem. 2012, 55, 6278 - 6293

39. Yunxiang Lu, Yingtao Liu, Haiying Li, Xiang Zhu, Honglai Liu, and Weiliang Zhu, Energetic Effects between Halogen Bonds and Anion-π or Lone Pair-π Interactions: A Theoretical Study, The Journal of Physical Chemistry A, 2012 116 (10), 2591-2597

40. Di Wang, Fei Wang, Yexiong Tan, Liwei Dong, Lei Chen, Weiliang Zhu*, Hongyang Wang*, Discovery of potent small molecule inhibitors of DYRK1A by structure-based virtual screening and bioassay, Bioorganic & Medicinal Chemistry Letters, 2012, 22, 168–171

41. Qiang Shao*, Jiye Shi, Weiliang Zhu*, Enhanced sampling molecular dynamics simulation captures experimentally suggested intermediate and unfolded states in the folding pathway of Trp-cage miniprotein. J. Chem. Phys. 2012, 137, 125013/1-125013/10.

42. Zhijian Xu, Guirui Yan, Gaihong Wang, Bo Li, Jianming Zhu, Peng Sun, Xiaodong Zhang, Cheng Luo, Heyao Wang*, Weiliang Zhu*, Combining pharmacophore, docking and substructure search approaches to identify and optimize novel B-Raf(V600E) inhibitors, Bioorg. Med. Chem. Lett. 2012, 22, 5428-5437.

43. Yunxiang Lu* , Yingtao Liu , Haiying Li, Xiang Zhu, Honglai Liu, Weiliang Zhu, Mutual Influence between Halogen Bonds and Cation–π Interactions: A Theoretical Study, ChemPhysChem ,2012, 13(8), 2154-2161

44. Haiying Li, Yunxiang Lu*, Yingtao Liu, Xiang Zhu, Honglai Liu, Weiliang Zhu, Interplay between halogen bonds and p–p stacking interactions: CSD search and theoretical study, Phys. Chem. Chem. Phys. 2012, 14, 9948-9955

45. Yunxiang Lu*, Yingtao Liu, Zhijian Xu, Haiying Li, Honglai Liu , Weiliang Zhu*, Halogen bonding for rational drug design and new drug discovery, Expert Opin. Drug Discov. 2012, 7(5), 375-383

46. Haiyan Cai, Zhijian Xu, Jie Tang, Ying Sun, Kaixian Chen, Heyao Wang*, Weiliang Zhu*, The essential role for aromatic cluster in the β3 adrenergic receptor. Acta Pharmacol Sin. 2012 ,33(8),1062-8

47. Deju Ye, Woo-Jin Shin, Ning Li, Wei Tang, Enguang Feng, Jian Li, Pei-Lan He,Jian-Ping Zuo*,Hanjo Kim , Ky-Youb Nam, Weiliang Zhu*, Baik-Lin Seong*, Kyoung Tai No ,Hualiang Jiang , Hong Liu*. Synthesis of C-4-modified zanamivir analogs as neuraminidase inhibitors and their anti-AIV activities. Eur J Med Chem. 2012 ,54,764-70

48. Yunxiang Lu*, Haiying Li, Xiang Zhu, Honglai Liu, Weiliang Zhu, Effects of solvent on weak halogen bonds: Density functional theory calculations,  International Journal of Quantum Chemistry, 2012, 112, 1421-1430

49. Jing Deng, Enguang Feng, Sheng Ma, Yan Zhang, Xiaofeng Liu, Honglin Li, Huang Huang, Jin Zhu, Weiliang Zhu, Xu Shen, Liyan Miao, Hong Liu, Hualiang Jiang, Jian Li. Design and Synthesis of Small Molecule RhoA Inhibitors: A New Promising Therapy for Cardiovascular Diseases? J. Med. Chem. 2011, 54, 4508-4522

50. Xue-lian Zhu, Hai-yan Cai, Zhi-jian Xu, Yong Wang, He-yao Wang, Ao Zhang and Wei-liang Zhu*. Classification of 5-HT(1A) receptor agonists and antagonists using GA-SVM method. Acta Pharmacol Sin., 2011, 32, 1424–1430

51. Lu Junming, Lu Yunxiang, Yang Subin, Zhu Weiliang*, Theoretical and crystallographic data investigations of noncovalent S···O interactions, Structural Chemistry, 2011, 24, 757-763

52. Jinan Wang¹, Weiliang Zhu¹, Guohui Li, Ulrich H. E. Hansmann, Velocity-scaling optimized replica exchange molecular dynamics of proteins in a hybrid explicit/implicit solvent. J Chem Phys. 2011 135(8):084115.

53. Yunxiang Lu*, Haiying Li, Xiang Zhu, Weiliang Zhu, Honglai Liu. How does halogen bonding behave in solution? A theoretical study using implicit solvation model. J. Phys Chem A. 2011, 115(17),4467-75

54. Zhijian Xu¹, Zheng Liu¹, Tong Chen¹, Tiantian Chen, Zhen Wang, Guanghui Tian, Jing Shi, Xuelan Wang, Yunxiang Lu, Xiuhua Yan, Guan Wang, Hualiang Jiang, Kaixian Chen, Shudong Wang, Yechun Xu*, Jingshan Shen*, Weilang Zhu*, Utilization of Halogen Bond in Lead Optimization: a Case Study of Rational Design of Potent Phosphodiesterase Type 5 (PDE5) Inhibitors, J. Med. Chem., 2011, 54 (15), 5607–5611

55. Junming Lu, Bo Zhang, Qingming Deng, Jinan Wang, Yunxiang Lu, Weiliang Zhu*, The Nature and Magnitude of Specific Halogen Bonds between Iodo-perfluorobenzene and Heterocyclic Systems, International Journal of Quantum Chemistry, 2011, 111, 2352-2358.

56. Jinan Wang, Huaiyu Yang, Zhili Zuo, Xiuhua Yan, Yong Wang, Xiaomin Luo, Hualiang Jiang, Kaixian Chen, Weiliang Zhu*, Molecular Dynamics Simulations on the Mechanism of Transporting Methylamine and Ammonia by Ammonium Transporter AmtB, J. Phys. Chem. B, 2010, 114, 15172–15179.

57. Weijun Xu; Gang Chen; Weiliang Zhu*, Zhili Zuo*, Molecular docking and Structure-Activity Relationship Studies on Benzothiazole based non-peptidic BACE-1 inhibitors, Bioorganic & Medicinal Chemistry Letters, 2010, 20, 6203-6207

58. Xiaodong Zhang, Guirui Yan, Yiming Li, Weiliang Zhu* and Heyao Wang*, DC260126, a small-molecular antagonist of GPR40, improves insulin tolerance but not glucose tolerance in obese Zucker rats, Biomedicine & Pharmacotherapy, 2010, 64(9), 647-651

59. Weijun Xu, Gang Chen, Hualiang Jiang, Weiliang Zhu*, Zhili Zuo*, Identification of a sub-micromolar Nonpeptide Inhibitor of β-secretase with low neural cytotoxicity through In-silico Screening, Bioorganic & Medicinal Chemistry Letters, 2010, 20, 5763-5766.

60. Haiyan Cai, Guirui Yan, Xiaodong Zhang, Olena Gorbenko, Heyao Wang*, Weiliang Zhu*, Discovery of highly selective inhibitors of human fatty acid binding protein 4 (FABP4) by virtual screening, Bioorganic & Medicinal Chemistry Letters, 2010, 20(12), 3675-9

61. Junming Lu, Yunxiang Lu*, Weiliang Zhu, Novel halogen bonding interactions between MH2 (M = Mg, Be) and HX (X = Cl, Br, I) molecules, Journal of Molecular Structure: THEOCHEM, 2010, 952, 84-89.

62. Shao-Yong Lu, Yong-Jun Jiang*, Jing Lv, Tian-Xing Wu, Qing-Sen Yu, Wei-Liang Zhu,* Molecular docking and molecular dynamics simulation studies of GPR40 receptor–agonist interactions , Journal of Molecular Graphics and Modelling, 2010, 28, 766–774.

63. Yunxiang Lu, Yong Wang and Weiliang Zhu*, Nonbonding interactions of organic halogens in biological systems: implications for drug discovery and biomolecular design, Physical Chemistry Chemical Physics, 2010, 12, 4543 - 4551.

64. Zhi Chen, Guanghui Tian, Zhen Wang, Hualiang Jiang, Jingshan Shen*, and Weiliang  Zhu*, Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity, J. Chem. Inf. Model., 2010, 50, 615-625

65. Hui Hu, Lingyan He, Zhen Gong, Ning Li, Yina Lu Qiwei Zhai, Hong Liu, Hualiang Jiang, Weiliang Zhu,* Heyao Wang*, A novel class of antagonists for the FFAs receptor GPR40, Biochem Biophys Res Commun, 2009, 390(3), 557-63

66. Kunqian Yu, Cheng Luo, Guangrong Qin, Zhijian Xu, Ning Li, Hong Liu, Xu Shen, Jianpeng Ma, Qinghua Wang, Caiguang Yang, Weiliang Zhu*, Hualiang Jiang*, Why are oseltamivir and zanamivir effective against the newly emerged influenza A virus (A/H1N1)?, Cell Research, 2009, 10, 1038

67. Yunxiang Lu, Yong Wang, Zhijian Xu, Xiuhua Yan, Xiaoming Luo, Hualiang Jiang, and Weiliang Zhu*, C−X•••H Contacts in Biomolecular Systems: How They Contribute to Protein-Ligand Binding Affinity? J. Phys. Chem. (B), 2009, 113, 12615–12621.

68. Yunxiang Lu, Ting Shi, Yong Wang, Huaiyu Yang, Xiuhua Yan, Xiaoming Luo, Hualiang Jiang, Weiliang Zhu*, Halogen Bonding — A Novel Interaction for Rational Drug Design, J. Med. Chem., 2009, 52, 2854–2862.

69. Zhili Zuo, Oi Wah Liew, Gang Chen, Pek Ching Jenny Chong, Siew Hui Lee, Kaixian Chen, Hualiang Jiang, Chum Mok Puah*, Weiliang Zhu*, Mechanism of NS2B-mediated activation of NS3pro in Dengue Virus: Molecular Dynamics Simulations and Bioassay Studies, J. Virology, 2009, 83, 1060-1070

70. Weijun Xu, Gang Chen, Oi Wah Liew, Zhili Zuo*, Hualiang Jiang, Weiliang Zhu*, Novel non-peptide b-secretase inhibitors derived from structure-based virtual screening and bioassay Bioorganic & Medicinal Chemistry Letters, 2009, 19, 3188–3192

71. He Huang, Qi Jia*, Jingui Ma, Guangrong Qin, Yingyi Chen, Yonghua Xi, Liping Lin, Weiliang Zhu, Jian Ding, Hualiang Jiang, Hong Liu*, Discovering novel quercetin-3-O-amino acid-esters as new class of Src tyrosine kinase inhibitors, Eur. J of Med Chem., 2009, 44, 1982-1988.

72. Lingyan He, Jiagao Cheng, Tao Wang, Caimei Li, Zhen Gong, Hong Liu*, Bu-Bing Zeng*, Hualiang Jiang, Weiliang Zhu*, Cation–p complexes formed between cyclooctatetraene and alkaline earth metals: Predicted and recorded NMR features, Chemical Physics Letters, 2008, 462, 45–48.

73. CHENG JiaGao, LUO XiaoMin, YAN XiuHua, LI Zhong, TANG Yun, JIANG HuaLiang1,& ZHU WeiLiang*, Research progress in cation-π interactions, Science in China Series B: Chemistry, 709-717 (2008)

74. CHENG JiaGao, ZHU WeiLiang*, WANG YanLi, YAN XiuHua, LI Zhong, TANG Yun& JIANG HuaLiang*, The open-close mechanism of M2 channel protein in influenza A virus: A computational study on the hydrogen bonds and cation-π interactions among His37 and Trp41 , Science in China Series B: Chemistry, 768-775 (2008)

75. Zhi-Li ZUO, Gang CHEN, Xiao-Min LUO, Chum-Mok PUAH*, Wei-Liang ZHU*, Kai-Xian CHEN, Hua-Liang JIANG. Pharmacophore-Directed Homology Modeling and MD Simulation of G-protein-Coupled Receptor: Study of Possible Binding Modes of the 5-HT2C Receptor Agonists, Acta Biochimica et Biophysica Sinica, 2007, 39, 413-422.

76. Wei Fu^1,3, Jianhua Shen¹, Xiaomin Luo¹, Weiliang Zhu¹*, Jiagao Cheng¹, Kunqian Yu¹, James M. Briggs², Guozhang Jin¹, Kaixian Chen¹ and Hualiang Jiang^1,4*, Dopamine D1 Receptor Agonist and D2 Receptor Antagonist Effects of the Natural Product (-)-Stepholidine (SPD): Molecular Modeling and Dynamics Simulations, Biophysics Journal,2007, 93, 1431-1441

77. Zhili Zuo, Chen Gang, Hanjun Zou, Puah Chum Mok, Weiliang Zhu*, Kaixian Chen, Hualiang Jiang,. Why does β-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies, Computational Biology and Chemistry, 2007, 31, 186–195

78. Chunshan  Gui, Weiliang Zhu*, Gang Chen, Xiaomin Luo, Oi Wah Liew, Chum Mok  Puah, Kaixian Chen, and Hualiang Jiang*, Understanding the Regulation Mechanisms of PAF Receptor by Agonists and Antagonists: Molecular Modeling and Molecular Dynamics Simulation Studies, Proteins: Structure, Function, and Bioinformatics, 2007, 67, 41–52

79. Jiagao Cheng, Zhen Gong, Weiliang Zhu*, Yun Tang, Weihua Li, Zhong Li, Hualiang Jiang*, Cation sitting in aromatic cages: ab initio computational studies on tetramethylamonium–(benzene)n (n=3-4) complexes, JOPC, 2007, 20, 448-453

80. Huaiyu Yang, Yechun Xu, Weiliang Zhu*, Kaixian Chen and Hualiang Jiang*, Detailed Mechanism for AmtB Conducting NH4+/NH3: Molecular Dynamics Simulations,  Biophysics Journal, 2007, 92, 877-885

81. Zhenshan Zhang, Mingyue Zheng, Li Du, Jianhua Shen, Xiaomin Luo^*, Weiliang Zhu^*, and Hualiang  Jiang,* Towards discovering dual functional inhibitors against both wild type and K103N mutant HIV-1 reverse transcriptases: molecular docking and QSAR studies on 4,1-benzoxazepinone analogues, Journal of Computer-Aided Molecular Design, 2006, 20, 281-293

82. Mingyue Zheng, Weiliang Zhu*, Kuqian Yu, Hualiang Jiang*, QSAR analyses on various neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR, Bioorg. Med. Chem., 2006, 20, 549–566

83. Hongxia Duan,¹ Zhen Gong,¹ Jiagao Cheng,² Weiliang Zhu,^1,2* Kaixian Chen,¹ Hualiang Jiang¹*, To induce an aromatic six-membered nitrogen ring via cation-π interaction, J. Phys. Chem. A., 2006, 110, 12236－12240

84. Lili Chen, Jian Li, Cheng Luo, Hong Liu, Weijun Xu, Gang Chen, Oi Wah Liew, Weiliang Zhu,* Chum  Mok Puah,* Xu Shen,* and Hualiang Jiang, Binding interaction of quercetin-3-β-galactoside and its synthetic derivatives with SARS-CoV 3CLpro: structure-activity relationship studies reveals salient pharmacophore features, Bioorg. Med. Chem. 2006, 14, 8295–8306

85. Jian Zhang, Kuanqin Yu, Weiliang Zhu*, Hualiang*, Neuraminidase pharmacophore model derived from diverse classes of inhibitors, Bioorg Med Chem Lett., 2006, 16: 3009-14

86. Rongjian Sa, WeiLiang Zhu,* JianHua Shen,* Zhen Gong, JiaGao Cheng, KaiXian Chen & HuaLiang Jiang,* How does ammonium dynamically interact with benzene in aqueous media? A first principle study using the Car-Parrinello molecular dynamics method. J. Phys. Chem. B , 2006, 110, 5094-5098

87. Zhen Gong, Hongying Shen, Weiliang Zhu,* Xiaomin Luo, Kaixian Chen &  Hualiang Jiang,* A computational study on electron transfer mechanism between alkaline earth metal atoms and cyclooctatetraene to form cation–p bonded complexes. Chemical Physics Letters, 2006, 423, 341-5

88. Jiagao Cheng, Weiliang Zhu,* Yun Tang, Yufang Xu, Zhong Li, Kaixian Chen & Hualiang Jiang,* Effect of cation–p interaction on NMR: A theoretical investigation on complexes of Li+, Na+, Be2+, and Mg2+ with aromatics. Chemical Physics Letters, 2006, 422, 455-460

89. Mingyue Zheng, Zhenshan Zhang, Weiliang Zhu,* Hong Liu, Xiaomin Luo, Kaixian Chen and Hualiang Jiang,* Essential structural profile of a dual functional inhibitor against cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX): Molecular docking and 3D-QSAR analyses on DHDMBF analogues, Bioorg. Med. Chem. 2006,14(10), 3428-37.

90. Jian Zhang, Yechun Xu, Jianhua Shen, Xiaomin Luo, Jiagao Chen, Kaixian Chen, Weiliang Zhu*, and Hualiang Jiang*, Dynamic Mechanism for the Autophosphorylation of CheA Histidine Kinase: Molecular Dynamics Simulations. J. AM. CHEM. SOC., 2005, 127, 11709-11719.

91. Suxin Zheng, Xiaomin Luo,* Gang Chen, Weiliang Zhu,* Jianhua Shen, Kaixian Chen, Hualiang Jiang*, A New Rapid and Effective Chemistry Space Filter in Recognizing Drug-like Database, Journal of Chemical Information and Modelling, 2005, 45, 856-862.

92. Yechun Xu, Jianhua Shen*, Weiliang Zhu*, Xiaomin Luo, Kaixian Chen,  Hualiang Jiang*, Influence of water molecule on cation-p interaction: ab initio second order Møller-Plesset perturbation theory (MP2) calculations. Journal of Physical Chemistry B, 2005, 109, 5945-5949.

93. Gang Chen, Suxin Zheng, Xiaomin Luo,* Jianhua Shen, Weiliang Zhu,* Hong Liu, Chunshan Gui, Jian Zhang, Mingyue Zheng, Chum  Mok Puah,  Kaixian Chen, Hualiang Jiang,* Focused Combinatorial Library Design Based on Structural Diversity, Drug-Likeness and Binding Affinity Score, Journal of Combinatorial Chemistry, 2005, 7(3) , 398-406

94. Zhili Zuo, Xiaomin Luo, Weiliang Zhu*, Jianhua Shen, Xu Shen, Hualiang Jiang*, Kaixian Chen, Molecular docking and 3D-QSAR studies on the binding mechanism of statine-based peptidomimetics with B-secretase, Bioorg. Med. Chem., 2005, 13(6), 2121-2131

95. Weiliang Zhu,^1,* Gang Chen,² Lihong Hu,³ Xiaomin Luo,¹ Chunshan Gui,^1,2 Cheng Luo,¹ Chum Mok Puah,² Kaixian Chen,¹ Hualiang  Jiang^1,* QSAR Analyses on Ginkgolides and Their Analogues Using CoMFA, CoMSIA and HQSAR, Bioorg. Med. Chem., 2005, 13, 313-322

96. Weiliang ZHU, Xiao-jian TAN, Chum  Mok PUAH, Xiao-Min LUO, Tong LIU, Hua-Liang JIANG, Kai-Xian CHEN, I Silman, J L Sussman, The Multiplicity, Strength, and Nature of the Interaction of Nucleobases with Alkaline and Alkaline Earth Metal Cations: A Density Functional Theory Investigation, Journal of Physical Chemistry (A), 2004, 108(18); 4008-4018.

97. Weiliang ZHU, Xiaojian Tan, Jianhua SHEN, Xiao-Min LUO, Feng Cheng, Chum Mok Puah, Ruyun Ji, Kai-Xian CHEN, Hua-Liang JIANG, Differentiation of Cation-π Bonding from Cation-π Intermolecular Interactions: A Quantum Chemistry Study using Density-Functional Theory and Morokuma Decomposition Methods, Journal of Physical Chemistry (A), 2003, 107(13); 2296-2303.

98. Weiliang ZHU, Tong LIU, Jianhua SHEN, Xiao-Min LUO, Xiao-Jian TAN, Chum Mok Puah, Hua-Liang JIANG, Kai-Xian CHEN, The interaction model between metal cation and tropylium: A quantum computational prediction, Chemical Physics Letter, 2002, 366/3-4, 267-273.

99. Wei-Liang ZHU, Chum Mok PUAH, Xiao-Jian TAN, Hua-Liang JIANG, Kai-Xian CHEN, Quantum Chemistry Investigation on the Dihydrogen Bond between Silicane and Ammonium, Journal of Physical Chemistry (A), 2001, 105, 426-431

100. Wei-liang Zhu, Chum Mok Puah, Kok Chin Ng, Hua-Liang Jiang, Xiao-Jian Tan and Kai-Xian Chen, Quantum chemical HF/4-31G calculations on buckminsterfullerene intermediates, Journal of Chemical Society (Perkin II), 2001,233-237

101. Xiao-jian TAN, Wei-Liang ZHU, Ming  CUI, Xiao-Min LUO, Jian-De GU, I  Silman, J L Sussman, Hua-Liang JIANG, Ru-Yuan JI, Kai-Xian CHEN, Noncovalent interaction or chemical bonding between alkaline earth cations and benzene? A quantum chemistry study using MP2 and density-functional theory methods, Chem. Phys. Letter, 2001, 349, 113-122.

102. Clifford E Felder, Hua-Liang JIANG, Wei-Liang ZHU, Kai-Xian CHEN, Simon A Botti, J L Sussman, Quantum/Classical mechanical comparison of cation-π interactions between tetramethylammonium and benzene, Journal of Physical Chemistry (A), 2001, 105, 1326-1333

103. Wei-Liang ZHU, Xiao-Jian TAN, Chum Mok PUAH, Jian-De GU, Hua-Liang JIANG, Kai-Xian CHEN, Clifford E Felder, I Silman, J L Sussman, How does ammonium interact with aromatic groups? A density functional theory (DFT/B3LYP) investigation, Journal of Physical Chemistry (A), 2000, 104, 9573-9580

104. Wei-Liang ZHU, Chum Mok PUAH, Xiao-Jian TAN, Hua-Liang JIANG, Kai-Xian CHEN and Ru-Yun JI, A Density functional theory (DFT) calculation of the geometry and vibrational spectrum of natural product, Ginkgolide B, J. Mol. Structure. (THEOCHEM), 2000, 528, 193-198

105. Wei-Liang ZHU, Hua-Liang JIANG, Chum Mok PUAH, Xiao-Jian TAN, Kai-Xian CHEN, Yang CAO, and Ru-Yun JI, Density functional theory (DFT) study on the interaction of ammonium (NH4+) and aromatic nitrogen heterocyclics, J. Chem. Soc. (Perkin II), 1999, (11): 2615-2622

106. Wei-Liang ZHU, Hua-Liang JIANG, Chum Mok PUAH, Xiao-Jian TAN, Kai-Xian CHEN, Yang CAO, Ru-Yun JI, Density Functional Theory (DFT) study on the interaction of ammoinium (NH₄⁺) and aromatic nitrogen heterocyclics, Journal of Chemical Society (Perkin II), 1999, 104, 2615-2622

107. Wei-Liang ZHU, Hua-Liang JIANG, Jian-Zhong CHEN, Jian-De GU, Kail-Xian CHEN, Yang CAO, Ru-Yun JI, Quantum chemistry study on the geometry and vibration spectrum of Huperzine A, Journal of Molecule Structure (THEOCHEM), 1999, 488: 21-28

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