Citation: Jianzhong Zhu, Cheng Chen, Jie Dong, Shasha Cheng, Guodong Li, Chunming Wang, Defang Ouyang, Chung-Hang Leung, Ligen Lin. Artificial intelligence-aided discovery of prolyl hydroxylase 2 inhibitors to stabilize hypoxia inducible factor-1α and promote angiogenesis[J]. Chinese Chemical Letters, ;2023, 34(2): 107514. doi: 10.1016/j.cclet.2022.05.028 shu

Artificial intelligence-aided discovery of prolyl hydroxylase 2 inhibitors to stabilize hypoxia inducible factor-1α and promote angiogenesis

Jianzhong Zhu ^{a, 1} ,
Cheng Chen ^{a, 1} ,
Jie Dong ^{a, b} ,
Shasha Cheng ^a ,
Guodong Li ^a ,
Chunming Wang ^a ,
Defang Ouyang ^a ,
Chung-Hang Leung ^a ,
Ligen Lin ^{a, *,}

a.
State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau 999078, China
b.
Xiangya School of Pharmaceutical Science, Central South University, Changsha 410083, China

ligenl@um.edu.mo

Received Date: 12 February 2022
Revised Date: 5 May 2022
Accepted Date: 11 May 2022
Available Online: 14 May 2022

Figures(4)

From ZINC database with a total of 1.8 million small molecules, four compounds are identified as prolyl hydroxylase 2 inhibitors through a virtual screening workflow that sequentially incorporates machine learning, molecular docking, and molecular dynamics. Among them, compound 103, (E)-5-(5-((2-(1H-tetrazol-5-yl)hydrazineylidene)methyl)furan-2-yl)isoindoline-1,3-dione, promotes the migration and capillary tube formation capacity of human umbilical vein endothelial cells through enhancing the stability of hypoxia inducible factor-1α and increasing the level of vascular endothelial growth factor.
- Machine learning,
- Virtual screening,
- PHD2,
- Angiogenesis,
- Wound healing
1. [1]
  G.L. Semenza, Cell 148 (2012) 399–408. doi: 10.1016/j.cell.2012.01.021
2. [2]
  I.R. Botusan, V.G. Sunkari, O. Savu, et al., Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 19426–19431. doi: 10.1073/pnas.0805230105
3. [3]
  X. Zhang, X. Yan, L. Cheng, et al., PLoS One 8 (2013) e84548. doi: 10.1371/journal.pone.0084548
4. [4]
  M.K. Teli, S. Kumar, D.K. Yadav, M.H. Kim, J. Biomol. Struct. Dyn. 39 (2021) 703–717. doi: 10.1080/07391102.2020.1714480
5. [5]
  H. Thangarajah, I.N. Vial, R.H. Grogan, et al., Cell Cycle 9 (2010) 75–79. doi: 10.4161/cc.9.1.10371
6. [6]
  S. Hu, C. Zhang, L. Ni, et al., Cell Death Dis. 11 (2020) 481. doi: 10.1038/s41419-020-2680-0
7. [7]
  J. Kalucka, A. Ettinger, K. Franke, et al., Mol. Cell. Biol. 33 (2013) 3426–3438. doi: 10.1128/MCB.00609-13
8. [8]
  G. Li, C.N. Ko, D. Li, et al., Nat. Commun. 12 (2021) 3363. doi: 10.1038/s41467-021-23448-7
9. [9]
  H.C.S. Chan, H. Shan, T. Dahoun, H. Vogel, S. Yuan, Trends Pharmacol. Sci. 40 (2019) 592–604. doi: 10.1016/j.tips.2019.06.004
10. [10]
  J. Du, J. Guo, D. Kang, et al., Chin. Chem. Lett. 31 (2020) 1695–1708. doi: 10.1016/j.cclet.2020.03.028
11. [11]
  Z. Yu, Z. Li, Q. Yu, et al., Chem. Biol. Drug Des. 95 (2020) 270–278. doi: 10.1111/cbdd.13640
12. [12]
  S. Li, C. Qin, S. Cui, et al., J. Med. Chem. 62 (2019) 2348–2361. doi: 10.1021/acs.jmedchem.8b01491
13. [13]
  H. Xiang, Y. Chen, J. Zhang, et al., Chin. Chem. Lett. 31 (2020) 1422–1426. doi: 10.1016/j.cclet.2020.03.017
14. [14]
  Z. Huang, J. Zhao, W. Deng, et al., Nat. Chem. Biol. 14 (2018) 1118–1126. doi: 10.1038/s41589-018-0150-0
15. [15]
  P. Vachal, S. Miao, J.M. Pierce, et al., J. Med. Chem. 55 (2012) 2945–2959. doi: 10.1021/jm201542d
16. [16]
  Y. Wu, N. Wang, Y. Lei, et al., Med. Chem. Comm. 7 (2016) 1271–1284. doi: 10.1039/C6MD00240D
17. [17]
  J. Huang, X. You, P. Xin, et al., Chin. Chem. Lett. 32 (2021) 1737–1742. doi: 10.1016/j.cclet.2020.12.006
18. [18]
  J. Fan, Y. Fan, Z. Wei, et al., Chin. Chem. Lett. 31 (2020) 1787–1791. doi: 10.1016/j.cclet.2020.03.065
19. [19]
  S. Wen, K. Zhang, Y. Li, et al., Chin. Chem. Lett. 31 (2020) 3153–3157. doi: 10.1016/j.cclet.2020.03.077
20. [20]
  R. Lou, F. Xu, Y. Xu, et al., Bioorg. Chem. 117 (2021) 105426. doi: 10.1016/j.bioorg.2021.105426
21. [21]
  G.C. Gurtner, S. Werner, Y. Barrandon, M.T. Longaker, Nature 453 (2008) 314–321. doi: 10.1038/nature07039
22. [22]
  R.J. Ruthenborg, J.J. Ban, A. Wazir, N. Takeda, J.W. Kim, Mol. Cells 37 (2014) 637–643. doi: 10.14348/molcells.2014.0150
1. [1]
  Qingyun Hu , Wei Wang , Junyuan Lu , He Zhu , Qi Liu , Yang Ren , Hong Wang , Jian Hui . High-throughput screening of high energy density LiMn_1-xFe_xPO₄ via active learning. Chinese Chemical Letters, 2025, 36(2): 110344-. doi: 10.1016/j.cclet.2024.110344
2. [2]
  Haijun Shen , Yi Qiao , Chun Zhang , Yane Ma , Jialing Chen , Yingying Cao , Wenna Zheng . A matrix metalloproteinase-sensitive hydrogel combined with photothermal therapy for transdermal delivery of deferoxamine to accelerate diabetic pressure ulcer healing. Chinese Chemical Letters, 2024, 35(12): 110283-. doi: 10.1016/j.cclet.2024.110283
3. [3]
  Yuting Wu , Haifeng Lv , Xiaojun Wu . Design of two-dimensional porous covalent organic framework semiconductors for visible-light-driven overall water splitting: A theoretical perspective. Chinese Journal of Structural Chemistry, 2024, 43(11): 100375-100375. doi: 10.1016/j.cjsc.2024.100375
4. [4]
  Jingwen Zhao , Jianpu Tang , Zhen Cui , Limin Liu , Dayong Yang , Chi Yao . A DNA micro-complex containing polyaptamer for exosome separation and wound healing. Chinese Chemical Letters, 2024, 35(9): 109303-. doi: 10.1016/j.cclet.2023.109303
5. [5]
  Zixing Xu , Ruiying Chen , Chuanming Hao , Qionghong Xie , Chunhui Deng , Nianrong Sun . Peptidome data-driven comprehensive individualized monitoring of membranous nephropathy with machine learning. Chinese Chemical Letters, 2024, 35(5): 108975-. doi: 10.1016/j.cclet.2023.108975
6. [6]
  Yunfen Gao , Liying Wang , Chufan Zhou , Yi Zhao , Hai Huang , Jun Wu . Low-dimensional antimicrobial nanomaterials in anti-infection treatment and wound healing. Chinese Chemical Letters, 2025, 36(3): 110028-. doi: 10.1016/j.cclet.2024.110028
7. [7]
  Xinyue Han , Yunhan Yang , Jiayin Lu , Yuxiang Lin , Dongxue Zhang , Ling Lin , Liang Qiao . Efficient serum lipids profiling by TiO₂-dopamin-assisted MALDI-TOF MS for breast cancer detection. Chinese Chemical Letters, 2025, 36(5): 110183-. doi: 10.1016/j.cclet.2024.110183
8. [8]
  Yang Xu , Le Ma , Yang Wang , Chunmeng Shi . Engineering strategies of biomaterial-assisted exosomes for skin wound repair: Latest advances and challenges. Chinese Chemical Letters, 2025, 36(1): 109766-. doi: 10.1016/j.cclet.2024.109766
9. [9]
  Zikang Hu , Hengjie Zhang , Zhengqiu Li , Tianbao Zhao , Zhipeng Gu , Qijuan Yuan , Baoshu Chen . Multifunctional photothermal hydrogels: Design principles, various functions, and promising biological applications. Chinese Chemical Letters, 2024, 35(10): 109527-. doi: 10.1016/j.cclet.2024.109527
10. [10]
  Yang Liu , Leilei Zhang , Kaixuan Liu , Ling-Ling Wu , Hai-Yu Hu . Penicillin G acylase-responsive near-infrared fluorescent probe: Unravelling biofilm regulation and combating bacterial infections. Chinese Chemical Letters, 2024, 35(11): 109759-. doi: 10.1016/j.cclet.2024.109759
11. [11]
  Chengde Wang , Liping Huang , Shanshan Wang , Lihao Wu , Yi Wang , Jun Dong . A distinction of gliomas at cellular and tissue level by surface-enhanced Raman scattering spectroscopy. Chinese Chemical Letters, 2024, 35(5): 109383-. doi: 10.1016/j.cclet.2023.109383
12. [12]
  Xiaoxiao Wang , Bolun Wang , Fenfen Ji , Jie Yan , Jiacheng Fang , Doudou Zhang , Ji Xu , Jing Ji , Xinran Hao , Hemi Luan , Yanjun Hong , Shulan Qiu , Min Li , Zhu Yang , Wenlan Liu , Xiaodong Cai , Zongwei Cai . Discovery of plasma biomarkers for Parkinson’s disease diagnoses based on metabolomics and lipidomics. Chinese Chemical Letters, 2024, 35(11): 109653-. doi: 10.1016/j.cclet.2024.109653
13. [13]
  Ze Zhang , Lei Yang , Jin-Ru Liu , Hao Hu , Jian-Li Mi , Chao Su , Bei-Bei Xiao , Zhi-Min Ao . Improved oxygen electrocatalysis at FeN₄ and CoN₄ sites via construction of axial coordination. Chinese Chemical Letters, 2025, 36(2): 110013-. doi: 10.1016/j.cclet.2024.110013
14. [14]
  Xiangyue Li , Dexin Zhu , Kunmin Pan , Xiaoye Zhou , Jiaming Zhu , Yingxue Wang , Yongpeng Ren , Hong-Hui Wu . Identifying key determinants of discharge capacity in ternary cathode materials of lithium-ion batteries. Chinese Chemical Letters, 2025, 36(5): 109870-. doi: 10.1016/j.cclet.2024.109870
15. [15]
  Yiwen Lin , Yijie Chen , Chunhui Deng , Nianrong Sun . Integration of resol/block-copolymer carbonization and machine learning: A convenient approach for precise monitoring of glycan-associated disorders. Chinese Chemical Letters, 2024, 35(12): 109813-. doi: 10.1016/j.cclet.2024.109813
16. [16]
  Yixia Zhang , Caili Xue , Yunpeng Zhang , Qi Zhang , Kai Zhang , Yulin Liu , Zhaohui Shan , Wu Qiu , Gang Chen , Na Li , Hulin Zhang , Jiang Zhao , Da-Peng Yang . Cocktail effect of ionic patch driven by triboelectric nanogenerator for diabetic wound healing. Chinese Chemical Letters, 2024, 35(8): 109196-. doi: 10.1016/j.cclet.2023.109196
17. [17]
  Jiliang Deng , Guoliang Shi , Zhihang Ye , Quan Xiao , Xiaoting Zhang , Lei Ren , Fangyu Yang , Miao Wang . Unveiling and swift diagnosing chronic wound healing with artificial intelligence assistance. Chinese Chemical Letters, 2025, 36(3): 110496-. doi: 10.1016/j.cclet.2024.110496
18. [18]
  Yao-Hua Gu , Yu Chen , Qing Li , Neng-Bin Xie , Xue Xing , Jun Xiong , Min Hu , Tian-Zhou Li , Ke-Yu Yuan , Yu Liu , Tang Tang , Fan He , Bi-Feng Yuan . Metabolome profiling by widely-targeted metabolomics and biomarker panel selection using machine-learning for patients in different stages of chronic kidney disease. Chinese Chemical Letters, 2024, 35(11): 109627-. doi: 10.1016/j.cclet.2024.109627
19. [19]
  Shiyang He , Dandan Chu , Zhixin Pang , Yuhang Du , Jiayi Wang , Yuhong Chen , Yumeng Su , Jianhua Qin , Xiangrong Pan , Zhan Zhou , Jingguo Li , Lufang Ma , Chaoliang Tan . 铂单原子功能化的二维Al-TCPP金属-有机框架纳米片用于增强光动力抗菌治疗. Acta Physico-Chimica Sinica, 2025, 41(5): 100046-. doi: 10.1016/j.actphy.2025.100046
20. [20]
  Xiaochen Zhang , Fei Yu , Jie Ma . 多角度数理模拟在电容去离子中的前沿应用. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-. doi: 10.3866/PKU.WHXB202311026

Get Citation

PDF

XML

Metrics

PDF Downloads(0)
Abstract views(824)
HTML views(60)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142