Hu QiaoYu
Associate Research Fellow
Innovation Center for AI and Drug Discovery
qyuhu@hsc.ecnu.edu.cn;15810011786@163.com
EDUCATONAL BACKGROUND
08/2014-06/2020 Department of Chemistry, University of Miami
Major: Computational Chemistry (Ph.D.), GPA 3.85
09/2011-06/2014 Institute of Process Engineering, University of Chinese Academy of Sciences
Major: Chemical Engineering (M.S.), GPA 3.5
09/2007-06/2011 School of Chemical Engineering, China University of Petroleum (Beijing)
Major: Chemical Engineering (B.E.)
Double degree: International Economy and Trade (B.E.)
Overall GPA: 86/100 Major GPA: 92/100
WORK EXPERIENCE
10/2020-10/2022 Postdoc, Shanghai Institute for Advanced Immunochemical Studies (SIAIS), ShanghaiTech University
11/2022-now Associate Research Fellow, Innovation Center for AI and Drug Discovery, ECNU
TECHNICAL SKILLS
1 Proficiency in using Linux system. Expertise in conducting QM and QM/MM (ONIOM) calculations through Gaussian and Gaussview softwares.
2 Proficiency in work with Python programming language. Ability to conduct machine learning especially deep learning using Tensorflow, Keras and Pytorch frameworks.
3 Proficiency in performing MD and FEC by GROMACS software. Capability to utilize enhanced sampling methods such as umbrella sampling, replica exchange and metadynamics. Familiarity with various force fields like Amber, Gromos and Charmm. Expertise in using various MD related softwares including Autodock Vina, Yasara and VMD.
4 Expertise in using Schrodinger software to perform tasks related to drug design and molecular simulation, such as virtual screening, homology modeling, binding site identification and so on.
5 Robust understanding of molecular modeling in the areas of computational chemistry, biology and biophysics. Familiarity with high performance computing environments.
6 Expertise in using chemical laboratory instruments associated with separation/purification and organic synthesis. Ability to separate the target product through chromatography and confirm the organic structure through NMR and MS. Familiarity with various characterization apparatuses such as ICP, UV, Fluorescence and IR.
AWARDS AND HONORS
12/2021-11/2022 Super Postdoctoral Incentive Program, Shanghai Human Resources and Social Security Bureau
06/2018-09/2018 Sam&Clara Summer Research Fellowship, University of Miami
09/2012-06/2014 China Science Group Environmental Scholarship, University of Chinese Academy of Sciences
09/2008-07/2009 Chinese Ocean Petroleum Scholarship, China University of Petroleum
09/2007-07/2008 National Scholarship, Ministry of Education, PRC
PUBLICATIONS
2012-2014 SCI Papers: (Co-authored 4 papers during Master, 2 of them are first author)
1. Qiaoyu Hu, Hari Paudyal, Junmei Zhao, Fang Huo, Katsutoshi Inoue, Huizhou Liu. Adsorptive recovery of vanadium(V) from chromium(VI) - containing effluent by Zr(IV)-loaded orange juice residue, Chemical Engineering Journal, 2014, 248, 79-88.
2. Qiaoyu Hu, Junmei Zhao, Fuchun Wang, Na Sui, Xiaoqin Wang, Fang Huo, Huizhou Liu. Selective extraction of vanadium from chromium by pure [C8mim][PF6]: an anion exchange process, Separation and Purification Technology, 2014, 131, 94-101.
3. Junmei Zhao, Qiaoyu Hu, Yingbo Li, Huizhou Liu. Efficient separation of vanadium and chromium by a novel ionic liquid-based synergistic extraction strategy, Chemical Engineering Journal, 2015, 264, 487-496.
4. Fuchun Wang, Junmei Zhao, Xuetuan Wei, Fang Huo, Wensong Li, Qiaoyu Hu, Huizhou Liu. Adsorption of rare earths (III) by calcium alginate - poly glumatic acid hybrid gels, Journal of Chemical Technology and Biotechnology, 2014, 89, 969-977.
2014-2020 SCI Papers: (Co-authored 9 papers during Ph.D., 4 of them are first author)
5. Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Joshua Zuchniarz, Rajeev Prabhakar. Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes. Frontiers in Chemistry, 2019, 7, 195.
6. Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Gaurav Sharma, Leonardo F. Serafim, Thomas J. Paul and Rajeev Prabhakar. Mechanisms of Peptide and Phosphoester Hydrolysis Catalyzed by Two Promiscuous Metalloenzymes (Insulin Degrading Enzyme and Glycerophosphodiesterase) and Their Synthetic Analogues. WIREs Computational Molecular Science, 2020, 10, e1466.
7. Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Rajeev Prabhakar. Degradation of a Main Plastic Pollutant Polyethylene Terephthalate by Two Distinct Proteases (Neprilysin and Cutinase-like Enzyme). Journal of Chemical Information and Modelling, 2021, 61, 764-776.
8. Qiaoyu Hu, Kevin Padron, Daiki Hara, Junwei Shi, Alan Pollack, Rajeev Prabhakar, Wensi Tao. Interactions of Urea-Based Inhibitors with Prostate-Specific Membrane Antigen for Boron Neutron Capture Therapy. ACS Omega, 2021, 6, 33354-33369.
9. Vindi M. Jayasinghe-Arachchige, Qiaoyu Hu, Gaurav Sharma, Thomas J. Paul, Marcus Lundberg, David Quiñonero, Tatjana N. Parac-Vogt and Rajeev Prabhakar. Hydrolysis of Chemically Distinct Sites of Human Serum Albumin (HSA) by Polyoxometalate (POM): A Hybrid QM/MM (ONIOM) Study. Journal of Computational Chemistry, 2019, 40, 51-61.
10. Gaurav Sharma, Qiaoyu Hu, Vindi M. Jayasinghe-Arachchige, Thomas Paul, Gerhard Schenk and Rajeev Prabhakar. Investigating Coordination Flexibility of Glycerophosphodiesterase (GpdQ) Through Interactions with Mono-, Di-, and Triphosphoester (NPP, BNPP, GPE, and Paraoxon) Substrates. Physical Chemistry Chemical Physics, 2019, 21, 5499-5509.
11. Thomas M. Carlino, Qiaoyu Hu, Amy M. Scott. Aggregate Induced Self-Assembly and Ultrafast Dynamics of Light-Harvesting D-A-A Polymorphs. Macromolecular Rapid Communications, 2018, 39, 1800391.
12. Gaurav Sharma, Vindi M. Jayasinghe-Arachchige, Qiaoyu Hu, Gerhard Schenk and Rajeev Prabhakar. The Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase. ACS Catalysis, 2020, 10, 3684-3696.
13. Mercedes M. A. Mazza, Shiori Yamazaki, Dieu X. Mai, Suyog Padgaonkar, Samuel Peurifoy, Ariane Goncalves, Yi-Lin Wu, Qiaoyu Hu, Amy M. Scott. Photoinduced charge recombination in dipolar D-A-A photonic liquid crystal polymorphs. Physical Chemistry Chemical Physics, 2017, 19, 4588-4596.
2020-now SCI Papers: (Co-authored 2 papers during Postdoc., 2 of them are first author)
14. Fenglei Li, Qiaoyu Hu, Ruofan Xiong, and Fang Bai. Computational drug design methods by deep learning algorithms. Chinese Journal of Nature, 2021, 43(5): 383-390.
15. Fenglei Li1, Qiaoyu Hu1, Xianglei Zhang1, Renhong Sun1, Zhuanghua Liu1, Sanan Wu, Siyuan Tian, Xinyue Ma, Zhizhuo Dai, Xiaobao Yang, Shenghua Gao, and Fang Bai. DeepPROTACs is a deep learning-based targeted degradation predictor for PROTACs. Nature Communications, 2022, 13, 7133.
16. Zhongneng Zhou, Zijing Chen, Xiu-Wen Kang, Yalin Zhou, Bingyao Wang, Siwei Tang, Shuhua Zou, Yifei Zhang, Qiaoyu Hu, Fang Bai, Bei Ding, and Dongping Zhong. 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, 2022, 119(26): e2203996119.
17. Pengxuan Ren1, Changyue Yu1, Ruxue Zhang1, Tianqing Nie1, Qiaoyu Hu1, Hui Li, Xianglei Zhang, Xueyuan Zhang, Shiwei Li, Lu Liu, Wenhao Dai, Jian Li, Yechun Xu, Haixia Su, Leike Zhang, Hong Liu, Fang Bai. Discovery, synthesis and mechanism study of 2, 3, 5-substituted [1, 2, 4]-thiadiazoles as covalent inhibitors targeting 3C-Like protease of SARS-CoV-2. European Journal of Medicinal Chemistry, 2023, 249, 115129.
18. Yanyan Diao, Dandan Liu, Huan Ge, Rongrong Zhang, Kexin Jiang, Kai Zhang, Rui Wang, Lili Zhu, Zhenjiang Zhao, Qiaoyu Hu, and Hongling Li. Macrocyclization of linear molecules by deep learning to facilitate macrocyclic drug candidates discovery. Nature Communications, Under revision.
19. Qiaoyu Hu1, Fenglei Li1, Shihang Wang, Zongquan Li, Ruitao Hu, Lianghe Mei, and Fang Bai. AutoFBDD: a fragment-based method for automatically generating small molecule inhibitors and PROTACs for target proteins. Under Preparation.
PATENTS
1. Fang Bai, Shenghua Gao, Hualiang Jiang, Fenglei Li, Qiaoyu Hu, Zhuanghua Liu. A neural network-based PROTACs degradation efficiency predictor and it’s construction method, 2021-9-07, China, 202111043888.3.