Discovery of SARS-CoV-2 entry disruptors by targeting the spike protein
Talk at 28th East Asia Joint Symposium on Biomedical Research, Shanghai, China
Education
- B.S. in college of life science, North East Agricultural University (NEAU), 2019
- Ph.D in Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University, 2024
Representative Work
- GeminiMol: a generic molecular representation model pre-trained on a miniaturized dataset (39,290), which incorporates conformational space profile into molecular representation learning. GitHub Advanced Science
- PPI-Miner: a motif-driven PPI identification method, that can be applied to discovering novel PPIs, the rational design of molecular glues, and protein vaccines. Using the PPI-Miner, we developed the first potential substrates database of CRBN, serving the rational design of molecular glue degraders. [Journal of Chemical Information and Modeling] [Online Database]
- Discovery of PPI disruptors by targeting the SARS-CoV-2 spike protein. [JMC] [APS]
Softwares and Databases
- GeminiMol, incorporating conformational space profile into molecular representation learning.
- GetPDB, downloading the single-chain protein structures for reverse docking or motif mining.
- PPI-Miner, a motif driven PPI mining method.
- CRBN substrates library, serving the rational design of the molecular glue.
- DeepSA, assessing the synthetic accessibility of small molecules, filtering out the hard-to-synthesize molecules.
Service and Leadership
- The Initiator of Schrödinger Chinese Community.
- The Developer of Bio-db page.
Academic Posters and Talks
Development and Application of Computational Methods for Rational Design of Molecular Glue
Poster at The 33rd CCS Congress, Qingdao, China
Publications
Antimicrobial resistance in clinical Ureaplasma spp. And Mycoplasma hominis and Structural Mechanisms Underlying Quinolone Resistance
Ting Yang, Lianlian Pan, Ningning Wu, Lin Wang, Zhen Liu, Yingying Kong, Zhi Ruan, Xinyou Xie, Jun Zhang, "Antimicrobial resistance in clinical Ureaplasma spp. And Mycoplasma hominis and Structural Mechanisms Underlying Quinolone Resistance." Antimicrobial Agents and Chemotherapy, 2020.
Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors
Zhenming Jin, Xiaoyu Du, Yechun Xu, Yongqiang Deng, Meiqin Liu, Yao Zhao, Bing Zhang, Xiaofeng Li, Leike Zhang, Chao Peng, Yinkai Duan, Jing Yu, Lin Wang, Kailin Yang, Fengjiang Liu, Rendi Jiang, Xinglou Yang, Tian You, Xiaoce Liu, Xiuna Yang, Fang Bai, Hong Liu, Xiang Liu, Luke Guddat, Wenqing Xu, Gengfu Xiao, Chengfeng Qin, Zhengli Shi, Hualiang Jiang, Zihe Rao, Haitao Yang, "Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors." Nature, 2020.
The structural study of mutation-induced inactivation of human muscarinic receptor M4
Jingjing Wang, Meng Wu, Lijie Wu, Yueming Xu, Fei Li, Yiran Wu, Petr Popov, Lin Wang, Fang Bai, Suwen Zhao, Zhi Liu, Tian Hua, "The structural study of mutation-induced inactivation of human muscarinic receptor M4." IUCrJ, 2020.
CKB inhibits epithelial-mesenchymal transition and prostate cancer progression by sequestering and inhibiting AKT activation
Zheng Wang, Mohit Hulsurkar, Lijuan Zhuo, Jinbang Xu, Han Yang, Samira Naderinezhad, Lin Wang, Guoliang Zhang, Nanping Ai, Linna Li, Jeffrey Chang, Songlin Zhang, Ladan Fazli, Chad Creighton, Fang Bai, Michael Ittmann, Martin Gleave, Wenliang Li, "CKB inhibits epithelial-mesenchymal transition and prostate cancer progression by sequestering and inhibiting AKT activation." Neoplasia (United States), 2021.
Identification of Potential Binding Sites of Sialic Acids on the RBD Domain of SARS-CoV-2 Spike Protein
Bingqian Li, Lin Wang, Huan Ge, Xianglei Zhang, Penxuan Ren, Yu Guo, Wuyan Chen, Jie Li, Wei Zhu, Wenzhang Chen, Lili Zhu, Fang Bai, "Identification of Potential Binding Sites of Sialic Acids on the RBD Domain of SARS-CoV-2 Spike Protein." Frontiers in Chemistry, 2021.
A multi-targeting drug design strategy for identifying potent anti-SARS-CoV-2 inhibitors
Peng Ren, Wei Shang, Wan Yin, Huan Ge, Lin Wang, Xiang Zhang, Bing Li, Hong Li, Ye Xu, Eric Xu, Hua Jiang, Li Zhu, Lei Zhang, Fang Bai, "A multi-targeting drug design strategy for identifying potent anti-SARS-CoV-2 inhibitors." Acta Pharmacologica Sinica, 2022.
Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue
Haofeng Wang, Yunjie Xiao, Xia Chen, Mengwen Zhang, Guangxin Sun, Feng Wang, Lin Wang, Hanxiao Zhang, Xiaoyu Zhang, Xin Yang, Wenling Li, Yi Wei, Deqiang Yao, Bing Zhang, Jun Li, Wen Cui, Fenghua Wang, Cheng Chen, Wei Shen, Dan Su, Fang Bai, Jinhai Huang, Sheng Ye, Lei Zhang, Xiaoyun Ji, Wei Wang, Zefang Wang, Mark Hochstrasser, Haitao Yang, "Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue." Nature Communications, 2022.
Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma
Qi Han, Xiang Zhang, Peng Ren, Liang Mei, Wei Lin, Lin Wang, Yu Cao, Kai Li, Fang Bai, "Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma." Acta Pharmacologica Sinica, 2022.
Discovery of potential small molecular SARS-CoV-2 entry blockers targeting the spike protein
Lin Wang, Yan Wu, Sheng Yao, Huan Ge, Ya Zhu, Kun Chen, Wen Chen, Yi Zhang, Wei Zhu, Hong Wang, Yu Guo, Pei Ma, Peng Ren, Xiang Zhang, Hui Li, Mohammad Ali, Wen Xu, Hua Jiang, Lei Zhang, Li Zhu, Yang Ye, Wei Shang, Fang Bai, "Discovery of potential small molecular SARS-CoV-2 entry blockers targeting the spike protein." Acta Pharmacologica Sinica, 2022.
PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method
Lin Wang, Feng Li, Xin Ma, Yong Cang, Fang Bai, "PPI-Miner: A Structure and Sequence Motif Co-Driven Protein-Protein Interaction Mining and Modeling Computational Method." Journal of Chemical Information and Modeling, 2022.
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers
Xin Liu, Jiale Yu, Siyu Tao, Beiyuan Yang, Shike Wang, Lin Wang, Fang Bai, Jie Zheng, "PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers." Bioinformatics (Oxford, England), 2022.
Rapamycin targets STAT3 and impacts c-Myc to suppress tumor growth
Le Sun, Yu Yan, Heng Lv, Jianlong Li, Zhiyuan Wang, Kun Wang, Lin Wang, Yunxia Li, Hong Jiang, Yaoyang Zhang, "Rapamycin targets STAT3 and impacts c-Myc to suppress tumor growth." Cell Chemical Biology, 2022.
Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms
Shiwei Li, Sanan Wu, Lin Wang, Fenglei Li, Hualiang Jiang, Fang Bai, "Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms." Current Opinion in Structural Biology, 2022.
Synthesis of maleimide-braced peptide macrocycles and their potential anti-SARS-CoV-2 mechanisms
Jian Li, Jina Sun, Xianglei Zhang, Ruxue Zhang, Qian Wang, Lin Wang, Leike Zhang, Xiong Xie, Chunpu Li, Yu Zhou, Jiang Wang, Gengfu Xiao, Fang Bai, Hong Liu, "Synthesis of maleimide-braced peptide macrocycles and their potential anti-SARS-CoV-2 mechanisms." Chemical Communications, 2022.
Target-Based Virtual Screening and LC/MS-Guided Isolation Procedure for Identifying Phloroglucinol-Terpenoid Inhibitors of SARS-CoV-2
Bo Hou, Yu Zhang, Han Liao, Li Fu, De Li, Xin Zhao, Jian Qi, Wei Yang, Geng Xiao, Lian Yang, Zheng Zuo, Lin Wang, Xiang Zhang, Fang Bai, Liu Yang, George Gao, Hao Song, Jiang Hu, Wei Shang, Jun Zhou, "Target-Based Virtual Screening and LC/MS-Guided Isolation Procedure for Identifying Phloroglucinol-Terpenoid Inhibitors of SARS-CoV-2." Journal of Natural Products, 2022.
Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications
Qian Wang, Lin Wang, Yumin Zhang, Xiang Zhang, Leike Zhang, Weijuan Shang, Fang Bai, "Probing the Allosteric Inhibition Mechanism of a Spike Protein Using Molecular Dynamics Simulations and Active Compound Identifications." Journal of Medicinal Chemistry, 2022.
DeepSA: a deep-learning driven predictor of compound synthesis accessibility
Shihang Wang, Lin Wang, Fenglei Li, Fang BAI, "DeepSA: a deep-learning driven predictor of compound synthesis accessibility." Journal of Cheminformatics, 2023.
Discovery, structural optimization, and anti-tumor bioactivity evaluations of betulinic acid derivatives as a new type of ROR$gamma$ antagonists
Lianghe Mei, Lansong Xu, Sanan Wu, Yafang Wang, Chao Xu, Lin Wang, Xingyu Zhang, Chengcheng Yu, Hualiang Jiang, Xianglei Zhang, Fang Bai, Chengying Xie, "Discovery, structural optimization, and anti-tumor bioactivity evaluations of betulinic acid derivatives as a new type of ROR$gamma$ antagonists." European Journal of Medicinal Chemistry, 2023.
Propofol exerts anti-anhedonia effects via inhibiting the dopamine transporter
Xiao-Na Zhu, Jie Li, Gao-Lin Qiu, Lin Wang, Chen Lu, Yi-Ge Guo, Ke-Xin Yang, Fang Cai, Tao Xu, Ti-Fei Yuan, Ji Hu, "Propofol exerts anti-anhedonia effects via inhibiting the dopamine transporter." Neuron, 2023.