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Dongqing Wei Profile Page
Dongqing Wei
Dongqing Wei
Professor
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34204573

Resume

Education and Degrees
B.S., Department of Chemistry, Normal University of Henan, Xinxiang, Henan, People's Republic of China, September 1978 - January 1982.
M.S., Department of Chemistry, Normal University of Henan, Xinxiang, Henan, People's Republic of China, January 1982 - January 1985.

Ph.D., Chemical Physics Program, University of Puerto Rico, Rio Piedras, Puerto Rico, USA, September 1985 - July 1987, thesis supervisor: Lesser Blum.

Post-doctorial Fellow, July 1987 - July 1990, Department of Chemistry, University of British Columbia, Vancouver, B.C., Canada, with Gren Patey.
Academic and Research Positions:

Professor, Feb. 2006- Present, Shanghai Jiaotong University, at the State Key Laboratory of Microbial Metabolism(Shanghai Jiaotong University),Acting Head, Department of Bioinformatics and Biostatistics, College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China

Haihe Professor, May 2003- Jan. 2006, appointed by the City of Tianjin at Tianjin Normal University, Director General, Tianjin Institute of Bioinformatics and Drug Discoverie

Research Scientist, Jan. 1992- May 2003, Centre de Recherche en Calcul Applique(CERCA, Research Center on Computation and its Application), Montreal, Quebec, and President of Montreal Institute of Technology

Research Associate, July 1990 - December 1992, Department of Chemistry, University of British Columbia, Vancouver, B.C., Canada, with Gren Patey associated with Network of Centers of Excellence in Molecular and Interfacial Dynamics

Membership and Professional Affiliations

Editor-in-Chief, “Interdisciplinary Sciences - Computational Life Sciences”;
One of Managing Editors: “J. Atomic and Molecular Sciences”;
Guest Editor, “Current Pharmaceutical Biotechnology”, “Current Drug Metabolism” ;
Review Editor: Frontiers in Genetics and Genomics;
Editorial Board:“Molecular Simulation”, “Journal of Molecular Graphics and Modeling”, “Journal of Atomic and Molecular Physics(In Chinese)” , “Journal of Biomedical Science and Engineering”, “International Journal of Biomedical Engineering and Consumer Health Informatics”, “The Open Drug Discovery Journal”, “J. Biomedical Research” , “Journal of Biophysical Chemistry”, “World Journal of Condensed Matter Physics", “Journal of Biotechnology and Biomaterials”, “Journal of Pharmaceutics”.

Research

Bioinformatics, as well as, quantum & statistical mechanical theory and computer simulation of molecular clusters, liquids, liquid crystals, solid/liquid interfaces, energetic materials and biologically interesting systems, for example: computer aided drug design, enzyme catalysis, solvation of biological molecules, reaction mechanism of energetic organic liquids(nitromethane), proton transfer dynamics, ab initio density functional theory(DFT), ab initio molecular dynamics(AIMD), Car-Parrinello MD(CPMD), combined quantum and molecular mechanic techniques(QM/MM), structure and dynamics of ferroelectric liquid crystals, double layers structures, dielectric relaxation and conductivity, dynamic solvation, equilibrium structure and thermodynamics of electrolytes and polar liquids.

Papers

1. IF: 9.02-Ruo-Xu Gu, Limin Angela Liu*, and Dong-Qing Wei*, “ Equilibrium of four binding states of anti-viral drug rimantadine in M2-lipid bilayer system”, J. Am. Chem. Soc., 133 (28), 10817–10825(2011).
2. IF: 7.33-Jing Chang, Peng Lian, Dong-Qing Wei*, Xiang-Rong Chen, Zizheng Gong and Qingming Zhang, “Thermal decomposition of the solid phase of nitromethane: Ab initio molecular dynamics simulations”, Phys. Rev. Lett. 105, 188302 -188305(2010).
3. .Cited 204 times, IF: 2.59 - K. C. Chou, D. Q. Wei, and W.Z. Zhong, “Binding Mechanism of Coronavirus Main Proteinase With Ligands and its Implication to Drug Design Against SARS”, Biochemical and Biophysical Research Communications, 308, 148(2003).
4. Cited 197 times, IF: 7.33 - D.Q. Wei and G.N. Patey, “Orientational Order in Simple Dipolar Liquids: Computer Simulation of a Ferroelectric Nematic Phase”, Phys. Rev. Letter, 68, 2043,(1992).
5. Cited 118 times, IF: 2.92 - D.Q. Wei and D.R. Salahub, “Hydrated Proton Clusters and Solvent Effects on the Proton Transfer Barrier: a Density Functional Study”, J. Chem. Phys., 101, 7633(1994).
6. Cited 116 times, IF: 2.86 - D.Q. Wei and G.N. Patey, “Ferroelectric Liquid Crystal and Solid Phases Formed by Strongly Interacting Dipolar Spheres”, Phys. Rev., A, 46, 7783, (1992).
7. Cited 96 times, IF 3.88 - Suzanne Sirois, Dong-Qing Wei, Qishi Du, Kuo-Chen Chou, “Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points”, J. Chem. Info. Comput. Sci., 44, 1111, 2004.
8. Cited 93 times, IF: 2.92 - D.Q. Wei, D.R. Salahub, “Hydrated Proton Clusters: Ab Initio Molecular Dynamics and Simulated Annealing”, J. Chem. Phys., 106, 6086(1997).
9. Cited 87 times, IF:9.02 - R.C. Dunbar, T.B., McMahon, D. Tholmann, D.S. Tonner, D.R. Salahub and D.Q. Wei, “Zero-pressure Thermal Radiation Induced Dissociation of Gas-phase Cluster Ions: Comparison of Theory and Experiment for (H2O)2Cl- and (H2O)3Cl- ”, J. Am. Chem. Soc., 117, 12819, (1995).
10. Cited 1 times, IF:3.82 - Jue Li, Dong-Qing Wei*, Jing-Fang Wang*, and Yi-Xue Li, “A Negative Cooperativity Mechanism of Huma n CYP2E1 Inferred from Molecular Dynamics Simulations and Free Energy Calculations”, J. Chem. Inf. Model., 51 (12), 3217–3225(2011).
11. IF:3.23 H. R. Arias, Ruo-Xu Gu, Dominik Feuerbach, Bao-Bao Guo, Yong Ye, and D.Q. Wei*, “Novel Positive Allosteric Modulators of the Human α7 Nicotinic Acetylcholine Receptor”, Biochemistry, 50, 5263–5278(2011).
12. IF:4.351 - Peng Lian, Dong-Qing Wei*, Jing-Fang Wang*, Kuo-Chen Chou, “An Allosteric Mechanism Inferred from Molecular Dynamics Simulations on Phospholamban Pentamer in Lipid Membranes”, PLoS ONE , 6, e18587(2011).
13. IF: 2.40 - Dong-Qing Wei*, Lin Gao, Jiao Zhang, Li-Wei Yan, Jin-He Hu, Lang Chen, Zi-Zheng Gong, Yong-Xin Guo, Yu Han, “Role of dipole elongation in orientationally ordered liquids”, Phys. Rev. E. 83, 061703-061707 (2011).
14. IF: 3.82 - Tao Zhang, Limin Liu*, David Lewis and D.Q. Wei*, "Long-Range Effects of a Surface Mutation on the Enzymatic Activity of Cytochrome P450 1A2", J. Chem. Info. Modeling, 51 , 1336–1346(2011).
15. IF:3.23 - Hugo R. Arias*, Ruo-Xu Gu, Dominik Feuerbach,and Dong-Qing Wei, “Different interaction between the agonist JN403 and the competitive antagonist methyllycaconitine with the human alpha7 nicotinic acetylcholine receptor”, Biochemistry, 49, 4169-4180(2010).

Invited reviews
16. Cited 86 times, IF:4.63 – KC Chou, D.Q. Wei and QS, Du, “Progress in computational approach to drug development against SARS”, Current Medicinal Chemistry, 13, 3263-3270( 2006).
17. Cited 26 times, IF: 4.11 - Jing-fang Wang, Dong-Qing Wei*, Kuo-chen Chou*, “Drug candidates from traditional chinese medicines”, Current Topics Med. Chem, 8, 1656-1665(2008).
18. Cited 21 times, IF: 4.11 - Jing-Fang Wang , Dong-Qing Wei*, Kuo-Chen Chou, “Pharmacogenomics and Personalized Use of Drugs”, Current Topics in Medicinal Chemistry, 8, 1573-1579(2008).
19. Cited 18 times, IF:3.47 - William Kem, Ferenc Soti, Susan LeFrancois, Kristin Wildeboer, Kelly MacDougall, Dong-Qing Wei, Kuo-Chen Chou and Hugo R. Arias, “The nemertine toxin anabaseine and its derivative DMXBA (GTS21): Chemical and pharmacological properties”, Marine Drugs 4, 55-273(2006).
20. Cited 15 times, IF: 4.63 - Jing-Fang Wang, Cheng-Cheng Zhang, , Jing-Yi Yan, Kuo-Chen Chou, Dong-Qing Wei* , “Structure of cytochrome P450s and personalized drug”, Current Medicinal Chem, 16, 232-244(2009).
21. Cited 2 times,IF: 1.52 - X. Guo, J.F. Wang, Y. Zhu, D.Q. Wei*, “Recent Progress on Computer-Aided Inhibitor Design of H5N1 Influenza A”, Current Computer Aided Drug Des. 6(2), 139-146(2010).
22. Cited 2 times ,IF: 1.52 - Suzanne Sirois, Rui Zhang, Weina Gao, Hui Gao, Yun Li and Dong-Qing Wei*, “Discovery of Potent anti-SARS-CoV MPro inhibitors”, Current Computer Aided Drug Design, 3, 341-352(2007).
23. IF: 4.774 -Ruo-Xu Gu, Yu-Qing Zhong and Dong-Qing Wei*, “Structural basis of agonist selectivity for different nAChR subtypes: insights from crystal structures, mutation experiments and molecular simulations”, Current Pharmaceutical Design, 17, 1652-1662(2011).
24. IF: 3.896, Qi Chen, Tao Zhang, Jing-Fang Wang* and Dong-Qing Wei*,“Advances in Human Cytochrome P450 and Personalized Medicine”, Current Drug Metabolism, 12, 436-444 (2011).
25. IF: 2.573 - Tao Zhang, Qi Chen, Li Li, Limin Angela Liu* and Dong-Qing Wei*,“ In silico prediction of CYP-mediated drug metabolism”, Combinatorial Chemistry & High Throughput Screening, 14, 388-395(2011).

Monographs

26. Dong-Qing Wei, Xijun Wang(editors), “Theory and Application of Computational Chemistry”, AIP Conference Proceedings Volume 1102, American Institute of Physics Press, 2009, ISBN: 9780735406377.
27. Limin Angela Liu, Dong-Qing Wei and Yixue li, “Interdisciplinary Research and Applications in Bioinformatics, Computational Biology, and Environmental Sciences”, ISBN: 9781609600648, IGI Global, 2010.
28. Limin Angela Liu, Dong-Qing Wei, Yixue Li and Huimin Lei, “Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications”, ISBN: 9781609604912, IGI Global, 2011.
29. Rong-Xiu Li, Dong-Qing Wei and Yan Feng, “The Protein Structure Simulation and Design”, Chinese Chemical Industrial, 2011, ISBN:9787122101839.
30. Dong-Qing Wei, Ruo-xu Gu, Peng Lian, Tao Zhang and Ying Wang, “Molecular Simulation and Computer Aided Drug Design”,Shanghai Jiaotong University Press,2012, ISBN:978-7-313-07980-0,Publishing Date: 2012-03-26.

Achievement

 Our papers were cited about 3000 times, two papers cited about 200 times, 20 papers cited more than 50 times, 33 papers cited more than 33 times, i.e., H factor 33

 We(D.Q. Wei and G.N Patey, 1992, Phys. Rev. letters) have found that strongly interacting dipolar spheres can form a ferroelectric nematic phase. This was the first demonstration that dipolar forces alone can create an orientationally ordered liquid state. It is also the first time that the existence of a ferroelectric nematic phase has been established for a model liquid. This discovery has created a new direction in search for new liquid crystal materials

 We made the first complete simulation of solid phase explosive reactions reported to date, where the solid NM undergoes chemical decomposition at about 2200 K under ambient pressure; 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2 and CNCNC, and the explosive reactions were complete by reaching its final and non-reacting state, which is of far-reaching implication for design and development of new energetic materials (Phys. Rev. Letters, 105, 188302 (2010)).

 We made the first computational work that provides both kinetic and thermodynamic energy information on the drug binding sites in the M2 proton channel. Our results provide a theoretical framework to interpret and reconcile existing and often conflicting results regarding these two binding sites, thus helping to expand our understanding of M2 drug binding, and may help guide the design and screening of novel drugs to combat the virus(JACS, 133, 10817(2011)).

 International Conference Chairman: Theory and Application of Computational Chemistry(1000 participants), Shanghai, 2008, IEEE Bioinformatics and Biomedical Engineering Conference, Shanghai, 2008(500 participants), 2008, International Conference on Computational and System Biology, Shanghai, 2009 and 2010(300 participants).

 Plenary talks in more than 50 international conferences.

 Invited talks at State University of New York, McGill University, University of Maine, University of Montreal, University of Calgary, University of Puerto Rico, Qinghua University, Beijing University, Taiwan University, Nanjing University, Xiamen University, Dalian Institute of Chemical Physics and many others.

 Published 5 monographs, 1 editorial, 10 invited review articles and 13 monograph/proceeding chapters.

 Participated in the software development of Docking, High Throughput Conformational Search, QSAR, 3D Pharmacophore Search, Similarity and Diversity in the frame work of MOE

 Independently implemented and developed the combined quantum and molecular mechanics (QM/MM) and ab initio molecular dynamics methods as practical tools of computational chemistry to study chemical reaction in complex environment. It expands significantly the scope of the deMon software package at Professor D. R. Salahub’s group.

 The octapeptide AVLQSGFR we designed is the most active in inhibiting replication of the SARS coronavirus compared with other compounds reported so far(EC50 is 2.7x10-2mg/L, and its selectivity index is more than 3704), one of the images of our BBRC paper was placed on the cover page of the Current Medicinal Chemistry(Vol. 11, No. 16, 2004).

 A new agonist of α7nAChR, gx50, was designed. It has been tested in vitro experiments that gx50 could combine with α7nAChR on nerve cells, induce depolymerization of Aβ, inhibit Aβ-induced neurocyte apoptosis, and suppress the release of TNF-α、IL-1β from microglia. In vivo experiments showed that it could improve the cognition ability in APP-Transgenic Mice. These results suggest that gx50 is a promising drug candidate for AD treatment.

 Performed the first ab initio molecular dynamics simulation to study the conformational dynamics of alanine dipeptides. It is found that conformation transformation between C5 and C7eq occurs at pecosecond(ps) time scale. Classical MD using most of the popular force fields does not yield a transition in a reasonable amount of simulation time.

 Developed complete and general molecular theories of liquid dynamics to deal with the complicated motions and couplings in liquids, mixtures and electrolyte solutions.

 Developed molecular theories of dielectric relaxation, frequency dependent conductivity and solvation dynamics, solves some long-standing problem, such as, the Onsager’s kinetic dielectric constant.