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Faculty and Staff
Faculty and Staff
Zhu Weiliang

Director of Drug Discovery and Design Center,PI
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555 Zu Chong Zhi Road,Zhang Jiang Hi-Tech Park, Pudong, Shanghai

I, as a principal investigator, joined the institute in 2004. My research focuses on 3 topics, e.g., (1) basic research and method development of drug design; (2) method development and application of computational biology, especially, for the simulation of protein function mechanism; (3) drug discovery and lead optimization study for proof-of-concept of drug design. I am interested in method and software development for drug design and computational biology. The aim of my research is to improve the efficacy and success rate of drug design through the deep understanding of intermolecular interactions between target protein and ligands. The target proteins studied in my group are mostly related to the diseases of tumor, diabetes, tuberculosis and so on. In the last 5 years, I obtained funding from central government and private companies, including National Natural Science Foundation, National Major Project for Drug Innovation, UCB Pharma and so on. We have published more than 100 papers, filed more than 20 patents and given more than 30 presentations in various scientific conferences.

1995 - 1998 Ph.D., Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China
1986 - 1988 M. Sci., Suzhou University, China
1979 - 1983 B. Sci., Yangzhou University, China

2009 - to date Director, Drug Discovery and Design Centre, Shanghai Institute of Materia Medica, CAS
2004 - to date Professor, Drug Discovery and Design Centre, Shanghai Institute of Materia Medica, CAS
1998 - 2004 Visiting Lecturer/Lecturer, Technology Centre for Life Sciences and School of Chemical and Life Sciences, Singapore Polytechnic
1983 - 1995 Lecturer, Yangzhou University

Research Directions

We focus on 3 topics 

  1. Basic theory of drug design and method development
  2. Computational method development and application for the simulation of biomolecule structuring and functioning
  3. Drug discovery and lead optimization study for proof-of-concept of drug design

We are particularly interested in the development of novel methods and software for drug design and computational biology, and their application with the combination of experimental technologies for the discovery of active compounds and lead optimization. The investigation strategy is: First, using computational methods to simulate the dynamic properties and biological function of target proteins, which allows the deep understanding of the intermolecular interaction between target protein and ligands; Second, combining computational simulation with experiment to perform proof-of-concept investigation of drug design, with the aim of improving the efficacy and success rate of drug design.

Social Titles
Member of the editorial board, Acta Pharmaceutica Sinica
Member of the computational chemistry committee (China)
25 invited presentations in domestic and international conferences

Awards & Honors


1. Basic Research and Method Development of CADD
(1)Halogen Bonding and Its Application in Drug Design
(2)Cation-Cation Interaction
(3)Lead Optimization Method Based On Target-Ligand Structure

2. Computational Biology and Simulation Method
(1)NUMD: A New Approach for Simulating Protein Conformational Change and Free Energy Profile
(2)Simulation on Structure-Function Relationship of Membrane Protein
(3)Polarizable Charge Parameters for Molecular Dynamics Simulation
(4)Protein Folding
(5)Predicting Drug Target Based on Protein Sequence

3. Drug Discovery and Lead Optimization for Proof-of-Concept of Drug Design
(1)Lead Compounds with Antitumor Activity
(2)Lead Compounds with anti-Diabetes Activity
(3)Compounds with anti-Tuberculosis Activity
(4)Protease Inhibitors of Dengue and SARS viruses
(5)Collaborating with other research groups, we performed virtual screening for discovering ligands for various target proteins related to the diseases like hepatitis B, asthma, and so on

Grants & Research Projects
  1. National 863,High performing simulation system for drug research and protein folding,Project Leader,2012-2015
  2. National Major Project for Drug Innovation,Drug leads based on the inhibitor of B-Raf V600E mutant,Project Leader,2012-2015
  3. National Natural Science Foundation,Scoring function of halogen bonding and its application in drug design,Project Leader,2013-2016
  4. National Natural Science Foundation,The simulation method development and application of large-scale protein conformational change,Project Leader (Qiang Shao),2014-2017
  5. National Natural Science Foundation,Drug repositioning based on virtual activity spectrum,Project Leader (Zhijian Xu) ,2014-2017
  6. Cooperation,Method development and application of computational biology,Project Leader,2012-2015
  7. Science and Technology Commission of Shanghai Municipality,Anticancer drug discovery and optimization based on various N-substituent of isoquinolones,Project Leader,2014-2017

  8. International collaboration,International collaboration on the key technologies of prevention and treatment of neglected tropical diseases in P.R. China,Project team member,2014-2017

  1. 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
  2. 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
  3. 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
  4. Qiang Shao, Jinan Wang, Jiye Shi, Weiliang Zhu, The universality of β-hairpin misfolding indicated by molecular dynamics simulations, The Journal of Chemical Physics, 2013, 139, 165103
  5. 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
  6. 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
  7. 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
  8. 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.
  9. 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
  10. 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
  11. 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
  12. 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.
  13. 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.
  14. 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
  15. 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
  16. 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.
  17. 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
  18. 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.
  19. 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.
  20. 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