Protein dynamics revealed by corase-grained, fine-grained and multiscale simulations approaches; Computer-aided Drug discovery; Algorithms, software and webservers development and applications; Rational design of enzymes.

2002.09-2006.06 Huaqiao University, China BSc in Bioengineering

2007.09-2010.06 Huaqiao University, China MSc in Biochemistry and Molecular Biology

2010.09-2014.09 Xiamen University, China PhD in Chemical Biology

   

2019.09-Present Research Associate Professor, Research Center for Computer-aided Drug Discovery at Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China    
2014.12-2019.08 Postdoctoral Associate, Department of Computational Systems and Biology at University of Pittsburgh, Pittsburgh, PA, USA    
2012.02-2014.07 Visiting Scholar, National Tsing Hua University, Taiwan

Google Scholar:

https://scholar.google.com/citations?hl=en&user=GZfKhjwAAAAJ&view_op=list_works&sortby=pubdate

1.  Xinxin Song^#, Zhuan Zhou^#, Hongchun Li^#, Yifan Xue, Ziyi Fu, Xinhua Lu, Ivet Bahar, Oliver Kepp, Mien-Chie Hung, Guido Kroemer and Yong Wan*. Pharmacological suppression of B7-H4 glycosylation restores antitumor immunity in immune-cold breast cancers. Cancer Discovery. 2020, (in press. Impact factor: 29.497; co-first).
2.  Bentley Wingert^#, James M. Krieger^#, Hongchun Li and Ivet Bahar*. Adaptability and Specificity: How do proteins balance opposing needs to achieve function? Current Opinion in Structural Biology. 2021, 67: 25-32 (Impact factor: 6.908).
3.  Hongchun Li^#, Fen Pei^#, D. Lansing Taylor and Ivet Bahar*. QuartataWeb: integrated chemical-protein-pathway mapping for polypharmacology and chemogenomics. Bioinformatics. 2020, 36(12): 3935–3937. (Impact factor: 5.610).
4.  Hongchun Li^#, Pemra Doruker^#, Guang Hu* and Ivet Bahar*. Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding. Biophysical Journal. 2020, 118(7): 1782-1794. (Impact factor: 3.854).
5.  Jiyoung Lee^#, James M. Krieger^#, Hongchun Li* and Ivet Bahar*. Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations. Protein Science. 2020, 29: 76-86 (Impact factor: 3.876; co-corresponding).
6.  Yan Zhang, Pemra Doruker, Burak Kaynak, She Zhang, James M. Krieger, Hongchun Li and Ivet Bahar*. Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior. Current Opinion in Structural Biology. 2020, 62: 14–21. (Impact factor: 6.908).
7.  Xiaoyan Zhuang^#, Aihui Zhang^#, Siyao Qiu, Chun Tang, Shiqiang Zhao, Hongchun Li, Yonghui Zhang, Yali Wang, Binju Wang, Baishan Fang* and Wenjing Hong*. Coenzyme coupling boosts charge transport through single bioactive enzyme junctions. iScience. 2020, 23(4): 101001. (Impact factor: 4.447).
8.  Junlong Chi^#, Hongchun Li^#, Zhuan Zhou, Javier Izquierdo-Ferrer, Yifan Xue, Cindy M. Wavelet, Gary E. Schiltz, Xinghua Lu, Ivet Bahar and Yong Wan*. A Novel Strategy to Block Mitotic Progression for Targeted Therapy. EBioMedicine. 2019, 49: 40-54. (Impact factor: 5.736; co-first).
9.  She Zhang^#, Hongchun Li^#, James M. Krieger^# and Ivet Bahar*. Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity. Molecular Biology and Evolution. 2019, 36(9): 2053–2068. (Impact factor: 11.062; co-first).
10.  Fen Pei^#, Hongchun Li^#, Bing Liu* and Ivet Bahar*. Quantitative Systems Pharmacological Analysis of Drugs of Abuse Reveals the Pleiotropy of Their Targets and the Effector Role of mTORC1. Frontiers in Pharmacology. 2019, 10: 191. (Impact factor: 4.225; co-first).
11.  Karolina Mikulska-Ruminska^#, Indira Shrivastava^#, James M. Krieger, She Zhang, Hongchun Li, Hülya Bayır, Sally E. Wenzel, Andrew P. VanDemark, Valerian E. Kagan and Ivet Bahar*. Characterization of differential dynamics, specificity, and allostery of lipoxygenase family members. Journal of Chemical Information and Modeling. 2019, 59(5): 2496-2508. (Impact factor: 4.549)
12.  Hongchun Li^#, Yuan-Yu Chang^#, Jiyoung Lee, Ivet Bahar* and Lee-Wei Yang*. DynOmics: dynamics of structural proteome and beyond. Nucleic Acids Research, 2017, 45: W374-W380. (Impact factor: 11.501).
13.  Hongchun Li^#, Nanaocha Sharma^#, Ignacio J. General, Gideon Schreiber* and Ivet Bahar*. Dynamic Modulation of Binding Affinity as a Mechanism for Regulating Interferon Signaling. Journal of Molecular Biology, 2017, 429(16): 2571-2589. (Impact factor: 4.760).
14.  Fen Pei, Hongchun Li, Mark J. Henderson, Steven A. Titus, Ajit Jadhav, Anton Simeonov, Murat Can Cobanoglu, Seyed H. Mousavi, Tongying Shun, Lee McDermott, Prema Iyer, Michael Fioravanti, Diane Carlisle, Robert M. Friedlander, Ivet Bahar, D. Lansing Taylor, Timothy R. Lezon, Andrew M. Stern & Mark E. Schurdak*. Connecting neuronal cell protective pathways and drug combinations in a Huntington’s disease model through the application of quantitative systems pharmacology. Scientific Reports, 2017, 7: 17803. (Impact factor: 3.998)
15.  Hongchun Li, Yuan-Yu Chang, Lee-Wei Yang* and Ivet Bahar*. iGNM 2.0: The Gaussian Network Model Database for Biomolecular Structural Dynamics. Nucleic Acids Research. 2016, 44(D1): D415-D422. (Impact factor: 11.501).
16.  Chin-Chi Chang, Md. Imran Khan, Kun-Lin Tsai, Hongchun Li, Lee-Wei Yang*, Ruey-Hwang Chou*, and Chin Yu*. Blocking the interaction between S100A9 and RAGE V domain using CHAPS molecule: A novel route to drug development against cell proliferation. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2016, 1864(11): 1558-1569. (Impact factor: 2.371)
17.  Hongchun Li^#, Shun Sakuraba^#, Aravind Chandrasekaran and Lee-Wei Yang*. Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs). Journal of Chemical Information and Modeling. 2014, 54(8): 2275-2285. (Impact factor: 4.549). 
18.  Jhen-Kai Li, Jiahn-Haur Liao, Hongchun Li, Chiao-I Kuo, Kai-Fa Huang, Lee-Wei Yang, Shih-Hsiung Wu and Chung-I Chang*. The N-terminal substrate-recognition domain of a LonC protease exhibits structural and functional similarity to cytosolic chaperones. Acta Crystallographica Section D: Biological Crystallography. 2013, 69: 1789-1797. (Impact factor: 5.266)
19.  Arun A. Gupta, Ruey-Hwang Chou, Hongchun Li, Lee-Wei Yang, Chin Yu*. Structural insights into the interaction of human S100B and basic fibroblast growth factor (FGF2): Effects on FGFR1 receptor signaling. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 2013, 1834(12): 2606-2619. (Impact factor: 2.371)
20.  Guangya Zhang*, Zhishan Chen, Hongchun Li and Kaizong Huang. Molecular dynamic simulation of elastin-like peptide. Computers and Applied Chemistry. 2011, 28(4): 399-402.
21.  Huihua Ge, Hongchun Li and Guangya Zhang*. Homology Modeling and Molecular Dynamic Simulation of Xylanase from Bacillus pumilus. Journal of Huaqiao University. 2011, 32(03): 296-299. 
22.  Hongchun Li, Guangya Zhang and Baishan Fang*. Using Pseudo Amino Acid Composition to Predict Hydrolase Subfamily. Journal of Huaqiao University. 2010, 31(3): 317-321. 
23.  Guangya Zhang, Hongchun Li, Jiaqiang Gao and Baishan Fang*. Protein piezophilicity: Solvent accessibility-based difference of amino acid in adaptation of proteins to high hydrostatic pressure. Acta Microbiologica Sinica. 2010, 50(5): 621-627.
24.  Guangya Zhang, Hongchun Li and Baishan Fang*. Discriminating acidic and alkaline enzymes using a random forest model with secondary structure amino acid composition. Process Biochemistry. 2009, 44(6): 654-660. (Impact factor: 2.952)
25.  Guangya Zhang, Hongchun Li, Jiaqiang Gao and Baishan Fang*. Influence of amino acid and dipeptide composition on protein stability of piezophilic microbes. Acta Microbiologica Sinica. 2009, 49(2): 198-203.
26.  Guangya Zhang, Hongchun Li, Jiaqiang Gao and Baishan Fang*. Predicting Lipase Types by Improved Chou&^#39;s Pseudo-Amino Acid Composition. Protein and Peptide Letters. 2008, 15(10): 1132-1137. (Impact factor: 1.156)
27.  Guangya Zhang, Hongchun Li and Baishan Fang*. Predicting the Cofactors of Oxidoreductases by the Modified Pseudo-amino Acid Composition. Chinese Journal of Biotechnology. 2008, 24(8): 1439-1445. 
28.  Guangya Zhang, Hongchun Li, Jiaqiang Gao and Baishan Fang*. Prediction of lipases types by different scale pseudo-amino acid composition. Chinese Journal of Biotechnology. 2008, 24(11): 1968-74. 
29.  Guangya Zhang, Hongchun Li and Baishan Fang*. Prediction of protein thermostability with a k-nearest neighbors algorithm. Computers and Applied Chemistry. 2008, 25(1): 39-41.

​

Evaluation system for the efficacy of antimicrobial peptides and the use thereof – (granted in China: CN106469251B) 2019

In silico design of peptides equilibrated in a lipid bilayer with partition free energies indicating probability of antimicrobial activity – (granted in the US: US10810329B) 2020

​Algorithm and software development for elastic network models (ENMs): DynOmics (ENM server), iGNM 2.0 (GNM database), IDD (intrinsic dynamics domains), ProDy-SignDy (mode conservation), aANM (coarse-grained sampling), CoMD and multiscale sampling.    

Structure-dynamics-function relationship analysis and regulation of protein: Conservation of normal modes of proteins, intramolecular communications and allostery of proteins; intrinsic dynamics of interferon-alpha receptors, AMPAR and toroidal proteins (e.g., DNA clamp) and regulations upon altering dynamics.    
Algorithm and software development for computer-aided drug design (CADD): developing QuartataWeb (polypharmacology and chemogenomics) and Pharmmaker (druggability simulations and pharmacophore modeling); high-throughput virtual screening; lead optimization.    
Drug discovery: design trypsin inhibitors, IFNARs inhibitor and Cdc20 PROTACs inhibitors; design novel antimicrobial peptides.    
Rational design of enzymes: altering substrate specificity of UndA; improving thermostability of Xylanase; improving activities of formate dehydrogenase and glycerol dehydrogenase; developing self-assembled multienzyme nanostructures; machine learning methods-based predictions on protein thermostability and enzyme classifications.    
Protein-protein interactions and function regulations: stability of immune checkpoint protein B7H4 regulated by ubiquitination and glycosylation affects tumor immunogenicity; cell proliferation and differentiation regulated by PPIs of S100B–EGFR and S100A9–RAGE.