|Asst Prof Zhang Dawei|
Division of Chemistry & Biological Chemistry
School of Physical & Mathematical Sciences
College of Science
- PhD (Theoretical & Computat'l Chemistry) New York Univrsity 2005
- MSc (Material Chemistry) Nankai University 1996
- BSc (Inorganic Chemistry) Nankai University 1993
|Zhang Dawei obtained his Ph.D. in Theoretical/Computational Chemistry from New York University Chemistry Department under Professor John Z.H. Zhang, developing a new algorithm to calculate the ab initio interaction energy between protein and drug molecule. After graduation in 2005, he worked as postdoctoral fellow and assistant research scientist under Prof. Sylvia Lee-Huang at New York University Langone Medical Center, Department of Biochemistry. His postdoctoral research focused on the discovery of natural anti-HIV and anti-obesity agents. His role is to identify the key components in plant extract using molecular docking simulation and examine their biological activities experimentally to confirm modeling predictions. This work represents a novel new field that merges computational chemistry, structural biology, bioinformatics, viral pathogenesis for rational development and targeted design of smart drugs. He joined NTU in June 2008.|
|The Dawei research group has two key research interests involving computational biology and molecular biology.
(1) Development of Force Field
We are collaborating with John Zhang's group at New York University to develop new force field containing polarized protein-specific charges (PPC) for molecular dynamics simulation of proteins by combining a recently developed fragment-based scheme, molecular fractionation with conjugate caps (MFCC), with continuum solvent model. Since the PPC is derived from first principal quantum solvation calculation of protein in a native (or a given) structure and thus correctly represents electronically polarized state of the protein and therefore provides accurate electrostatic interaction near the native structure. Extensive researches will be carried out to investigate the effects of PPC on protein folding (especially for folding thermodynamics), protein-protein interaction, protein-ligand interaction, and protein-ligand docking.
(2) Structure-Function of CAM
Structure-based virtual ligand screening computation is performed on a natural compound library to discover novel classes of PPAR-delta agonists. The free energies of binding with PPAR-delta will be predicted by using linear interaction energy (LIE) method. The real binding affinity values of putative candidates will be measured by adipogenesis assay and whether they are agonists or antagonists or partial agonists will be determined by measuring the expression of PPAR-delta during adipocyte differentiation. After confirming the validity of the predicted binding energy values and also their binding conformations by comparing the predicted values with the experimental data, we will then further analyze the binding conformations of PPAR-delta agonists to identify important structural determinants that would favour PPAR-delta binding. The goal of our research in the field of complementary and alternative medicine (CAM) is to identify novel natural PPAR-delta agonists as promising new drugs in the fight against obesity.
|Research Grant |
- A*STAR Science and Engineering Research Council - Public Sector Funding (2012-)
- Academic Research Fund Tier 1 (2009-)
- Academic Research Fund Tier 1 (2012-)
- College of Science Collaborative Research Award (2012-)
- Start Up Grant (2008-)
|Current Projects |
- Ab Initio Folding of Helix Peptides Using Adaptive Hydrogen Bond-Specific Charge Scheme
- Antimicrobial Materials Against Drug-Resistant Bacteria: Design, Spectroscopic Characterization and Computational Modelling
- Application of MFCC-derived Atomic Charges
- HL9 Based D-Peptide Design as HIV Entry Inhibitor
- Virtual screening on natural products for discovering PPAR? agonist
- Yossa Dwi Hartono, Angelina Noviani Lee, Sylvia Lee-Huang, Dawei Zhang. (2011). Computational Study of Bindings of HL9, a Nonapeptide Fragment of Human Lysozyme, to HIV-1 fusion protein gp41. Bioorganic and Medicinal Chemistry Lettres, .
- Caiyi Wei, Zeyu Liu, Ye Mei, Dawei Zhang. (2011). Docking of raltegravir to HIV-1 integrase structure ensemble. Journal of Theoretical and Computational Chemistry, .
- Angelina Noviani Lee, Yossa Dwi Hartono, Tiedong Sun, Min Li Leow, Xue-wei Liu, Xuri Huang, Dawei Zhang*. (2010). Molecular dynamics studies of human receptor molecule in hemagglutinin of 1918 and 2009 H1N1 influenza viruses. Journal of molecular modeling, .
- Li L. Duan, Ye Mei, Dawei Zhang, Qing G. Zhang, and John Z. H. Zhang. (2010). Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds. J. Am. Chem. Soc., 132(32), 11159.
- Caiyi Wei, Ye Mei, Dawei Zhang. (2010). Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields. Chemical Physics Letters, 495, 121.