Principal investigator
Name:
Fang BaiAssociate Professor , PhD, Associate Professor
Position:
Affiliation:
School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies
Honor:
Education Background:
- 2004/09-2009/07, Dalian University of Technology, BE; BA
- 2009/09-2014/05, Dalian University of Technology, Ph.D
Working Experience:
- 2014/08-2019/05, Rice University, Postdoctoral Reserach Fellow
- 2019/05-2019/09, UT Health Science Center at Houston, Assistant Professor of Research
- 2019/10-2025/04, ShanghaiTech University, Assistant Professor (TENURE-TRACK)
- 2025/04-present, Shanghaitech University, Associate Professor(TENURED)
Group Introduction
Research Area:
Drug Design and Developmen
Research Interests:
Research in the Bai Group (the Lab of Drug Design)combines elements of computational drug design, theory of biophysics, molecular biology and cell biology to devise efficient drug design methods.
We are particularly interested in :1) developing methods for designing molecular glues/PROTACs, fragment-based drug design, peptide designing, PPI prediction, and protein conformational sampling by introducing artificial intelligence algorithms. 2)identifying and optimizing novel therapeutic agents for treating serious diseases,i.e., human cancer and virus infection.

Representative Publications (*First Author, # Corresponding Author)
- 1. Li, Fenglei*; Hu, Qiaoyu; Zhang, Xianglei; Sun, Renhong; Liu, Zhuanghua; Wu, Sanan; Tian, Siyuan; Ma, Xinyue; Dai, Zhizhuo; Yang, Xiaobao#; Gao, Shenghua#; Bai, Fang#.DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs.NATURE COMMUNICATIONS. 21 Nov 2022. 13(1).
- 2. Li, Jian*; Sun, Jina; Zhang, Xianglei; Zhang, Ruxue; Wang, Qian; Wang, Lin; Zhang, Leike; Xie, Xiong; Li, Chunpu; Zhou, Yu; Wang, Jiang; Xiao, Gengfu#; Bai, Fang#; Liu, Hong#.Synthesis of maleimide-braced peptide macrocycles and their potential anti-SARS-CoV-2 mechanisms.CHEMICAL COMMUNICATIONS. 01 Dec 2022.
- 3. Wang, Qian#*; Wang, Lin; Zhang, Yumin; Zhang, XiangLei; Zhang, Leike; Shang, Weijuan#; Bai, Fang#.Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications.JOURNAL OF MEDICINAL CHEMISTRY. 24 Feb 2022. 65(4).
- 4. Li, Shiwei*; Wu, Sanan; Wang, Lin; Li, Fenglei; Jiang, Hualiang; Bai, Fang#.Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms.CURRENT OPINION IN STRUCTURAL BIOLOGY. Apr 2022. 73.
- 5. Karmi, Ola*; Marjault, Henri-Baptiste; Bai, Fang; Roy, Susmita; Sohn, Yang-Sung; Yahana, Merav Darash; Morcos, Faruck; Ioannidis, Konstantinos; Nahmias, Yaakov; Jennings, Patricia A.; Mittler, Ron; Onuchic, Jose N.#; Nechushtai, Rachel#.A VDAC1-mediated NEET protein chain transfers [2Fe-2S] clusters between the mitochondria and the cytosol and impacts mitochondrial dynamics.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 15 Feb 2022. 119(7).
- 6. Han, Qi-lei*; Zhang, Xiang-lei; Ren, Peng-xuan; Mei, Liang-he; Lin, Wei-hong; Wang, Lin; Cao, Yu; Li, Kai#; Bai, Fang#.Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma.ACTA PHARMACOLOGICA SINICA. Oct 2022.
- 7. Ren, Peng-xuan*; Shang, Wei-juan*; Yin, Wan-chao*; Ge, Huan*; Wang, Lin*; Zhang, Xiang-lei; Li, Bing-qian; Li, Hong-lin; Xu, Ye-chun; Xu, Eric H.; Jiang, Hua-liang; Zhu, Li-li#; Zhang, Lei-ke#; Bai, Fang#.A multi-targeting drug design strategy for identifying potent anti-SARS-CoV-2 inhibitors.ACTA PHARMACOLOGICA SINICA. Feb 2022.
- 8. Wang, Lin*; Wu, Yan*; Yao, Sheng*; Ge, Huan*; Zhu, Ya; Chen, Kun; Chen, Wen-zhang; Zhang, Yi; Zhu, Wei; Wang, Hong-yang; Guo, Yu; Ma, Pei-xiang; Ren, Peng-xuan; Zhang, Xiang-lei; Li, Hui-qiong; Ali, Mohammad A.; Xu, Wen-qing; Jiang, Hua-liang; Zhang, Lei-ke#; Zhu, Li-li#; Ye, Yang#; Shang, Wei-juan#; Bai, Fang#.Discovery of potential small molecular SARS-CoV-2 entry blockers targeting the spike protein.ACTA PHARMACOLOGICA SINICA. Apr 2022.
- 9. Wang, Lin*; Li, Feng-lei; Ma, Xin-yue; Cang, Yong; Bai, Fang#.PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method.JOURNAL OF CHEMICAL INFORMATION AND MODELING. 01 Nov 2022.
- 10. Bai, Fang*; Liu, Kangdong*; Li, Huiliang*; Wang, Jiawei; Zhu, Junsheng; Hao, Pei; Zhu, Lili; Zhang, Shoude; Shan, Lei; Ma, Weiya; Bode, Ann M.; Zhang, Weidong#; Li, Honglin#; Dong, Zigang#.Veratramine modulates AP-1-dependent gene transcription by directly binding to programmable DNA.NUCLEIC ACIDS RESEARCH. 2018. 46(2):546-557.
- 11. Iosub-Amir, Anat*; Bai, Fang*; Sohn, Yang-Sung; Song, Luhua; Tamir, Sagi; Marjault, Henri-Baptiste; Mayer, Guy; Karmi, Ola; Jennings, Patricia A.; Mittler, Ron; Onuchic, Jose N.#; Friedler, Assaf#; Nechushtai, Rachel#.The anti-apoptotic proteins NAF-1 and iASPP interact to drive apoptosis in cancer cells.CHEMICAL SCIENCE. 2019. 10(3):665-673.
- 12. Bai, Fang*; Pi, Xiaoping*; Li, Ping; Zhou, Pingzheng; Yang, Huaiyu; Wang, Xicheng; Li, Min; Gao, Zhaobing#; Jiang, Hualiang#.A Statistical Thermodynamic Model for Ligands Interacting With Ion Channels: Theoretical Model and Experimental Validation of the KCNQ2 Channel.FRONTIERS IN PHARMACOLOGY. 2018. 9.
- 13. Bai, Fang*; Morcos, Faruck; Cheng, Ryan R.; Jiang, Hualiang#; Onuchic, Jose N.#.Elucidating the druggable interface of protein-protein interactions using fragment docking and coevolutionary analysis.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2016. 113(50):8051-8058.
- 14. Bai, Fang*; Morcos, Faruck*; Sohn, Yang-Sung; Darash-Yahana, Merav; Rezende, Celso O.; Lipper, Colin H.; Paddock, Mark L.; Song, Luhua; Luo, Yuting; Holt, Sarah H.; Tamir, Sagi; Theodorakis, Emmanuel A.; Jennings, Patricia A.#; Onuchic, Jose N.#; Mittler, Ron#; Nechushtai, Rachel#.The Fe-S cluster-containing NEET proteins mitoNEET and NAF-1 as chemotherapeutic targets in breast cancer.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2015. 112(12):3698-3703.
- 15. Bai, Fang*; Liao, Sha*; Gu, Junfeng; Jiang, Hualiang; Wang, Xicheng; Li, Honglin#.An Accurate Metalloprotein-Specific Scoring Function and Molecular Docking Program Devised by a Dynamic Sampling and Iteration Optimization Strategy.JOURNAL OF CHEMICAL INFORMATION AND MODELING. 2015. 55(4):833-847.
- 16. Bai, Fang*; Xu, Yechun; Chen, Jing; Liu, Qiufeng; Gu, Junfeng; Wang, Xicheng; Ma, Jianpeng; Li, Honglin#; Onuchic, Jose N.#; Jiang, Hualiang#.Free energy landscape for the binding process of Huperzine A to acetylcholinesterase.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2013. 110(11):4273-4278.
- 17. Bai, Fang*; Liu, Hongyan*; Tong, Linjiang; Zhou, Wei; Liu, Li; Zhao, Zhenjiang; Liu, Xiaofeng; Jiang, Hualiang; Wang, Xicheng#; Xie, Hua#; Li, Honglin#.Discovery of novel selective inhibitors for EGFR-T790M/L858R.BIOORGANIC & MEDICINAL CHEMISTRY LETTERS. 2012. 22(3):1365-1370.
- 18. Bai, Fang*; Liu, Xiaofeng; Li, Jiabo; Zhang, Haoyun; Jiang, Hualiang; Wang, Xicheng#; Li, Honglin#.Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods.BMC BIOINFORMATICS. 2010. 11.
- 19. Jin, Zhenming*; Du, Xiaoyu*; Xu, Yechun*; Deng, Yongqiang*; Liu, Meiqin*; Zhao, Yao; Zhang, Bing; Li, Xiaofeng; Zhang, Leike; Peng, Chao; Duan, Yinkai; Yu, Jing; Wang, Lin; Yang, Kailin; Liu, Fengjiang; Jiang, Rendi; Yang, Xinglou; You, Tian; Liu, Xiaoce; Yang, Xiuna; Bai, Fang; Liu, Hong; Liu, Xiang; Guddat, Luke W.; Xu, Wenqing; Xiao, Gengfu; Qin, Chengfeng; Shi, Zhengli; Jiang, Hualiang#; Rao, Zihe#; Yang, Haitao#.Structure of M-pro from SARS-CoV-2 and discovery of its inhibitors.NATURE. 09 Apr 2020. 582(7811):289–293.
- 20. Lipper, Colin H.*; Stofleth, Jason T.*; Bai, Fang; Sohn, Yang-Sung; Roy, Susmita; Mittler, Ron; Nechushtai, Rachel; Onuchic, Jose N.#; Jennings, Patricia A.#.Redox-dependent gating of VDAC by mitoNEET.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2019. 116(40):19924-19929.
- 21. Dai, Wenhao*; Zhang, Bing*; Jiang, Xia-Ming*; Su, Haixia*; Li, Jian; Zhao, Yao; Xie, Xiong; Jin, Zhenming; Peng, Jingjing; Liu, Fengjiang; Li, Chunpu; Li, You; Bai, Fang; Wang, Haofeng; Cheng, Xi; Cen, Xiaobo; Hu, Shulei; Yang, Xiuna; Wang, Jiang; Liu, Xiang; Xiao, Gengfu; Jiang, Hualiang; Rao, Zihe; Zhang, Lei-Ke#; Xu, Yechun#; Yang, Haitao#; Liu, Hong#.Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.SCIENCE. 19 Jun 2020. 368(6497):1331-1335.
- 22. Wang, Haofeng*; Xiao, Yunjie; Chen, Xia; Zhang, Mengwen; Sun, Guangxin; Wang, Feng; Wang, Lin; Zhang, Hanxiao; Zhang, Xiaoyu; Yang, Xin; Li, Wenling; Wei, Yi; Yao, Deqiang; Zhang, Bing; Li, Jun; Cui, Wen; Wang, Fenghua; Chen, Cheng; Shen, Wei; Su, Dan; Bai, Fang; Huang, Jinhai; Ye, Sheng; Zhang, Lei; Ji, Xiaoyun; Wang, Wei; Wang, Zefang; Hochstrasser, Mark; Yang, Haitao.Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue.NATURE COMMUNICATIONS. 25 Mar 2022. 13(1):1608.
- 23. Zhou, Zhongneng*; Chen, Zijing; Kang, Xiu-Wen; Zhou, Yalin; Wang, Bingyao; Tang, Siwei; Zou, Shuhua; Zhang, Yifei; Hu, Qiaoyu; Bai, Fang; Ding, Bei#; Zhong, Dongping#.The nature of proton-coupled electron transfer in a blue light using flavin domain.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 28 Jun 2022. 119(26).
- 24. Bai, Fang#*; Jiang, Hualiang.Computationally Elucidating the Binding Kinetics for Different AChE Inhibitors to Access the Rationale for Improving the Drug Efficacy.JOURNAL OF PHYSICAL CHEMISTRY B. Sep 2022.
- 25. Liu, Haixia*; Mi, Qianglong; Ding, Xinyu; Lin, Chencen; Liu, Linyi; Ren, Chaowei; Shen, Shu Ting; Shao, Yu Bao; Chen, Jinju; Zhou, Yongqi; Ji, Liting; Zhang, Heqiao; Bai, Fang#; Yang, Xiaobao#; Yin, Qianqian#; Jiang, Biao#.Discovery and characterization of novel potent BCR-ABL degraders by conjugating allosteric inhibitor.EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY. 15 Dec 2022. 244.
- 26. Tan, Zheqiong*; Xiao, Lanbo*; Tang, Min*; Bai, Fang; Li, Jiangjiang; Li, Liling; Shi, Feng; Li, Namei; Li, Yueshuo; Du, Qianqian; Lu, Jingchen; Weng, Xinxian; Yi, Wei; Zhang, Hanwen; Fan, Jia; Zhou, Jian; Gao, Qiang; Onuchic, Jose N.; Bode, Ann M.; Luo, Xiangjian#; Cao, Ya#.Targeting CPT1A-mediated fatty acid oxidation sensitizes nasopharyngeal carcinoma to radiation therapy.THERANOSTICS. 2018. 8(9):2329-2347.
- 27. Yim, Kendrick H.*; Prince, Thomas L.; Qu, Shiwei; Bai, Fang; Jennings, Patricia A.; Onuchic, Jose N.; Theodorakis, Emmanuel A.*; Neckers, Leonard#*.Gambogic acid identifies an isoform-specific druggable pocket in the middle domain of Hsp90 beta.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2016. 113(33):4801-4809.
- 28. Darash-Yahana, Merav*; Pozniak, Yair*; Lu, Mingyang*; Sohn, Yang-Sung; Karmi, Ola; Tamir, Sagi; Bai, Fang; Song, Luhua; Jennings, Patricia A.; Pikarsky, Eli; Geiger, Tamar; Onuchic, Jose N.#; Mittler, Ron#; Nechushtai, Rachel#.Breast cancer tumorigenicity is dependent on high expression levels of NAF-1 and the lability of its Fe-S clusters.PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2016. 113(39):10890-10895.
- 29. Wang, Chong*; Jiang, Yi; Ma, Jinming; Wu, Huixian; Wacker, Daniel; Katritch, Vsevolod; Han, Gye Won; Liu, Wei; Huang, Xi-Ping; Vardy, Eyal; McCorvy, John D.; Gao, Xiang; Zhou, X. Edward; Melcher, Karsten; Zhang, Chenghai; Bai, Fang; Yang, Huaiyu; Yang, Linlin; Jiang, Hualiang; Roth, Bryan L.; Cherezov, Vadim; Stevens, Raymond C.#; Xu, H. Eric#.Structural Basis for Molecular Recognition at Serotonin Receptors.SCIENCE. 2013. 340(6132):610-614.
Group Member and Photo
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Name:Xianglei Zhang
Position:Postdoct
Duration:2020.08-present
Email:
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Name:Pengxuan Ren
Position:Postgraduate Student
Duration:2019.09-present
Email:
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Name:Lin Wang
Position:Postgraduate Student
Duration:2019.09-present
Email:
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Name:Ruofan Xiong
Position:Postgraduate Student
Duration:2019.09-present
Email:
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Name:Shuai Yan
Position:Undergraduate Student
Duration:2020.01-present
Email:
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Name:Lianghao Zhao
Position:Undergraduate Student
Duration:2020.1-presnet
Email:
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Name:Wenjing Wu
Position:Undergraduate Student
Duration:2020.02-present
Email:
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Name:Guo Chen
Position:Undergraduate Student
Duration:2020.2-present
Email:
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Name:WenXuan Li
Position:Undergraduate Student
Duration:2020.2-present
Email:
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Name:Xuyang Li
Position:Undergraduate Student
Duration:2020.05-present
Email:
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Name:Huiqiong Li
Position:Visiting Student
Duration:2019.11-2020.7
Email:
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Name:Bingqian Li
Position:Visiting Student
Duration:2020.7-2020.9
Email:
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