Dr. Yan Li received her Ph.D. at Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences in 2010. In July of the same year, she joined the Key Laboratory Bioorganic Chemistry in the institute for scientific research. She was promoted to associate researcher in May, 2013. Since October 2019, she has been working in the School of Pharmacy at Fudan University, as a full associate professor.
Dr. Li’s research interests mainly focus on (1) developing key theories and methods in structure-based drug design; (2) exploring the characteristic interaction patterns on protein-protein interactions and developing small-molecule regulators for them; (3) using molecular modeling to guide the optimization of the lead compounds. She has published over 30 SCI papers in peer-reviewed journals and has hosted two projects supported by the National Natural Science Foundation of China.
Structure-based drug design
Protein-ligand binding affinityprediction
Lead discovery and optimization
Small-molecular regulators targetingprotein-protein interactions
2005.9-2010.7
Ph. D.State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
Major: Molecular modeling and computer-aided drug design
Advisor: Prof. Wang
2001.9-2005.7
B. S.Department of Chemistry, University of Science and Technology of China, Hefei, Anhui province, China
Major: Chemistry
Advisor: Prof. Youcheng Liu, Academician of Chinese Academy of Sciences
Professional Experiences
2019.10-now
Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
Position: Associate Professor
2013.5-2019.9
State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
Position: Associate Professor
2010.7-2013.4
State Key Laboratory of Bioorganic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
Position: Research Associate
Grants & Projects
1.General program of NSFC (21472226) Development of Customized Scoring Functions for Proteases, 2015.1.1-2018.12.31
2.Youth program of NSFC (21102168) Mining of Characteristic Interaction Patterns on Protein-Protein Binding Interface and Its Applications in Structure-Based Drug Design, 2012.1-2014.12.31
3.Amgen’s Postdoc Fellowship Research Program (2017.11-2019.10), Structure-Based Design of Small-Molecule Modulators for Class B GPCRs
4.Amgen’s Postdoc Fellowship Research Program (2015.11-2017.10), Computational Methods for Structure-Based Design of GPCR Ligands
5.MSD Postdoc Fellowship Research Program (2013.9-2016.9) Development of Customized Scoring Functions for Structure-Based Drug Design
Selected Publications（latest 5 yrs，<20 papers）
1. Li, Y.*; Gao, Y.; Holloway, M. K.; Wang, R.* Prediction of the favorable hydration sites in a protein binding pocket and its application to scoring function formulation. J. Chem. Inf. Model. 2020, in press, DOI: 10.1021/acs.jcim.9b00619.
2. Li, Y.*; Sun, Y.; Song, Y.; Dai, D.; Zhao, Z.; Zhang, Q.; Zhong, W.; Hu, L. A.; Ma, Y.; Li, X.*; Wang, R.* Fragment-based computational method for designing GPCR ligands. J. Chem. Inf. Model. 2020, in press, DOI: 10.102/acs.jcim.9b00699.
3.Li, Q.; An, R.; Xu, Y.; Zhou, M.; Li, Y.*; Guo, C.*; Wang, R.* Synthesis of (1,3,4-thiadiazol-2-yl)-acrylamide derivatives as potential antitumor agents against acute leukemia cells. Bioorg. Med. Chem. Lett. 2020, 30, 127114.
4.Yang, Q.; Su, M.; Li, Y.; Wang, R.* Revisiting the Relationship Between Correlation Coefficient, Confidence Level, and Sample Size. J. Chem. Inf. Model. 2019, 59, 4602-4612.
5.Su, M.; Yang, Q.; Du, Y.; Feng, G.; Liu, Z.; Li, Y.*; Wang, R.* Comparative assessment of scoring functions: The CASF-2016 update. J. Chem. Inf. Model. 2019, 59, 895-913.
6. Li, Y.; Su, M.; Liu, Z.; Li, J.; Liu, J.; Han, L.; Wang, R.* Assessing protein-ligand interaction scoring functions with the CASF-2013 benchmark. Nat. Protocols 2018, 3, 666-680.
7.Han, L.; Yang, Q.; Liu, Z.; Li, Y.; Wang, R.* Development of a new benchmark for assessing the scoring functions applicable to protein-protein interactions. Future Med. Chem. 2018, 10, 1555-1574.
8.Wu, S.; He, Y.; Qiu, X.; Yang, W.; Liu, W.; Li, X.; Li, Y.; Shen, H.; Wang, R.; Yue, Z.; Zhao, Y. Targeting the potent Beclin 1-UVRAG coiled-coil interaction with designed peptides enhances autophagy and endolysosomal trafficking. Proc. Natl. Acad. Sci. USA 2018, 115, E5669-E5678.
9.Naowarojna, N.; Huang, P.; Cai, Y.; Song, H.; Wu, L.; Cheng, R.; Li, Y.; Wang, S.; Liu, H.; Zhang, L.; Zhou, J.; Liu, P. In vitro reconstitution of the remaining steps in ovothiol A biosynthesis: C-S lyase and methyltransferase reactions. Org. Lett. 2018, 20, 5427-5430.
10.Jiang, Y.; Qian, F.; Yang, J.; Liu, Y.; Dong, F.; Xu, C.; Sun, B.; Chen, B.; Xu, X.; Li, Y.; Wang, R.; Yang, S. CRISPR-Cpf1 assisted genome editing of Corynebacterium glutamicum. Nat. Commun. 2017, 8:15179.
11.Liu, Z.; Su, M.; Han, L.; Liu, J.; Yang, Q.; Li, Y.*; Wang, R*. Forging the basis for developing protein-ligand interaction scoring functions. Acc. Chem. Res. 2017, 50, 302-309.
12.Liu, J.; Su, M.; Liu, Z.; Li, J.; Li, Y.*; Wang, R.* Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints. BMC Bioinformatics 2017, 18:343.
13. Li, Y.; Zhao, Z.; Liu, Z.; Su, M.; Wang, R.* AutoT&T v2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. J. Chem. Inf. Model. 2016, 56, 435-453.
14.Xu, X.; Chen,, J.; Wang, Q.; Duan, C.; Li, Y.; Wang, R.; Yang, S.* Mutagenesis of Key Residues in the Binding Center of l-Aspartate-b-Semialdehyde Dehydrogenase from Escherichia coli Enhances Utilization of the Cofactor NAD(H). ChemBioChem 2016, 17, 56-64.
15.Chen, W.; Li, Y.; Li, J.; Wu, L.; Li, Y.; Wang, R.; Deng, Z.; Zhou, J.* An unusual UMP C-5 methylase in nucleoside antibiotic polyoxin biosynthesis. Protein Cell 2016, 7, 673-683.
16.Liu, Z.; Li, Y.; Han, L.; Li, J.; Liu, J.; Zhao, Z.; Nie, W.; Liu, Y.; Wang, R.* PDB-wide collection of binding data: current status of the PDBbind database. Bioinformatics 2015, 31, 405-412.
17.Liu, Z.; Li, Y.; Han, L.; Li, J. Liu, J.; Zhao, Z.; Nie, W.; Liu, Y.; Wang, R.* Cross-mapping of protein-ligand binding data between ChEMBL and PDBbind. Mol. Informatics 2015, 34, 568-576.
