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AIDD8121, Research Methodology and Ethics

AIDD8299, Thesis

Dr. Jingjing Guo obtained her Ph.D. degree in medicinal chemistry from Lanzhou University in 2015. She joined the Center for Artificial Intelligence Driven Drug Discovery (AIDD) at Macao Polytechnic University in 2022. She has made a series of innovative achievements in computational biology and drug discovery. Now she has published more than 80 SCI papers, including Chemical Reviews, Elife, Angewandte Chemie International Edition, WIREs Computational Molecular Science, and other international authoritative journals. She has served as Associate Editor of Current Research in Structural Biology since January 2024.

ORCID | Scopus | Google Scholar | ResearchGate

  • Current Employer/Organization

    Macao Polytechnic University

  • Current Position

    Professor

    Macao Polytechnic University

  • Subjects Taught

    AIDD8121, Research Methodology and Ethics

    AIDD8299, Thesis

  • Education

    2009-2015: Ph.D. in Medicinal Chemistry, Lanzhou University, China
    2013-2015: Visiting Ph.D. student in Biophysics, Florida State University, United States
    2005-2009: B.S. in Chemistry, Hebei Normal University, China

  • Research Interests

    Ø  Artificial intelligence and healthcare big data 

    Ø  Artificial intelligence and drug discovery

    Ø  Rational design of enzymes

  • Work Experience

    2022-present: Professor, Macao Polytechnic University
    2019-2022: Professor, Nanjing Agricultural University, China
    2017-2019: Research Fellow, Nanyang Technological University, Singapore
    2015-2018: Associate Professor, Henan Normal University, China

  • Publications

    Selected publications:

    1. Ye, Y.; Jiang, H.; Xu, R.; Wang, S.; Zheng, L.*; Guo, J.* The INSIGHT platform: Enhancing NAD(P)-dependent specificity prediction for co-factor specificity engineering. International Journal of Biological Macromolecules 2024, 135064. http://dx.doi.org/10.1016/j.ijbiomac.2024.135064
    2. Xu, R.; Pan, Q.; Zhu, G.; Ye, Y.; Xin, M.; Wang, Z.; Wang, S.; Li, W.; Wei, Y.; Guo, J.*; Zheng, L.* ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction. Protein Science 2024, 33, e5097. http://dx.doi.org/10.1002/pro.5097
    3. Li, X.; Zhang, F.; Zheng, L.*; Guo, J.* Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction. JOURNAL OF HAZARDOUS MATERIALS 2024, 475, 134828. http://dx.doi.org/10.1016/j.jhazmat.2024.134828
    4. Yuan, L.; Guo, J.* PharmaRedefine: A database server for repurposing drugs against pathogenic bacteria. METHODS 2024, 227, 78-85. http://dx.doi.org/10.1016/j.ymeth.2024.05.011

    5. Shi, L.; Zhao, W.; Jiu, Z.; Guo, J.*; Zhu, Q.; Sun, Y.; Zhu, B.; Chang, J.; Xin, P.* Redox-Regulated Synthetic Channels: Enabling Reversible Ion Transport by Modulating the Ion-Permeation Pathway. Angew Chem Int Ed Engl 2024, e202403667. http://dx.doi.org/10.1002/anie.202403667

    6. Bao, Y.; Jia, F.; Li, M.; Xu, R.; Xie, Y.; Zhang, F.*; Guo, J.* Characterizing the Molecular Mechanism of the Lethal C423D Mutation in FgMyoI: A Molecular Perspective. J Agric Food Chem 2024, 72, 1539-1549. http://dx.doi.org/10.1021/acs.jafc.3c08648

    7. Li, M.; Zhang, X.; Li, S.; Guo, J.* Unraveling the Interplay of Extracellular Domain Conformational Changes and Parathyroid Hormone Type 1 Receptor Activation in Class B1 G Protein-Coupled Receptors: Integrating Enhanced Sampling Molecular Dynamics Simulations and Markov State Models. ACS Chem Neurosci 2024, 15, 844-853. http://dx.doi.org/10.1021/acschemneuro.3c00747

    8. Jiao, F.; Cui, W.; Wang, P.; Tong, H. H. Y.; Guo, J.*; Tao, J.* Synergistic inhibition mechanism of quinazolinone and piperacillin on penicillin-binding protein 2a: a promising approach for combating methicillin-resistant Staphylococcus aureus. J Biomol Struct Dyn 2024, 1-13. http://dx.doi.org/10.1080/07391102.2024.2330708

    9. Guo, J*; Bao, Y; Li, M; Li, S; Xi, L; Xin, P; Wu, L; Liu, H; Mu, Y. Application of computational approaches in biomembranes: From structure to function. Wiley Interdiscip. Rev. Comput. Mol. Sci., 2023, 13, e1679.
    10. Xin, P.*; Xu, L.; Dong, W.; Mao, L.; Guo, J.*; Bi, J.; Zhang, S.; Pei, Y.; Chen, C. P.*, Synthetic K(+) Channels Constructed by Rebuilding the Core Modules of Natural K(+) Channels in an Artificial System. Angew. Chem. Int. Ed. Engl., 2023, 62, e202217859.
    11. M. Li; Y. Bao; Xu, R.; Li, M.; Xi, L.*; Guo, J.*, Understanding the Allosteric Modulation of PTH1R by a Negative Allosteric Modulator. Cells, 2023, 12, 41.
    12. Xi, L*; Shi, A; Shen, T; Wang, G; Wei, Y; Guo, J*. Licraside as novel potent FXR agonist for relieving cholestasis: structure-based drug discovery and biological evaluation studies. Front. in Pharmacol. 2023, 14, 1197856.
    13. Li, M.; Bao, Y.; Li, M.; Guo, J.*, GPCR Allostery: A View from Computational Biology. Curr. Med. Chem. 2023, 30, 4533.
    14. Li, M.;  Li, M.; Guo, J.*, Molecular Mechanism of Ca(2+) in the Allosteric Regulation of Human Parathyroid Hormone Receptor-1. J. Chem. Inf. Model. 2022, 62, 5110-5119.
    15. J. Guo; H. X. Zhou, Allosteric activation of SENP1 by SUMO1 beta-grasp domain involves a dock-and-coalesce mechanism. Elife, 2016, 5, e18249.
    16. J. Guo; H.-X. Zhou, Protein allostery and conformational dynamics. Chem. Rev., 2016, 116, 6503.

  • Description

    Research Interests:

    • Artificial intelligence and healthcare big data 
    • AI-empowered drug repositioning and drug discovery
    • AI-driven protein design and modification


    Tools and Resources:

    • EcoToxPred [1]: capable of predicting ecotoxicity, specifically the toxicity of molecules to bees and the ecological degradation potential of molecules.
    • INSIGHT [2]: an expansive dataset and predictive model for NAD(P)H coenzyme specificity.
    • ThermoLink [3]: a comprehensive dataset containing the effect of disulfide bonds on the protein thermostability.
    • PharmaRedefine [4]: a database server for repurposing drugs against pathogenic bacteria.
    • ReverseDocking [5]: Benchmarking Reverse Docking through AlphaFold2 Human Proteome. AF2 human proteome binding site predictions with PointSite. 


    1. Li X, Zhang F, Zheng L, Guo J. Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction. J. Hazard. Mater., 2024, 475, 134828
    2. Ye Y, Jiang H, Xu R, Wang S, Zheng L, Guo J. The INSIGHT platform: Enhancing NAD(P)-dependent specificity prediction for co-factor specificity engineering. Int. J. Biol. Macromol., 2024, 278, 135064
    3. Xu R, Pan Q, Zhu G, Ye Y, Xin M, Wang Z, Wang S, Li W, Wei Y, Guo J, Zheng L. ThermoLink: Bridging disulfide bonds and enzyme thermostability through database construction and machine learning prediction. Protein Sci., 2024, 33, e5097
    4. Yuan L, Guo J. PharmaRedefine: A database server for repurposing drugs against pathogenic bacteria. Methods, 2024, 227, 78
    5. Luo Q, Wang S, Li H Y, Zheng L, Mu Y, Guo J. Benchmarking reverse docking through AlphaFold2 human proteome. Protein Sci., 2024, 33, e5167

  • Journal papers

    Recently published papers:

    1.  Shi, L.; Zhao, W.; Jiu, Z.; Guo, J.*; Zhu, Q.; Sun, Y.; Zhu, B.; Chang, J.; Xin, P.* Redox-Regulated Synthetic Channels: Enabling Reversible Ion Transport by Modulating the Ion-Permeation Pathway. Angew Chem Int Ed Engl 2024, e202403667. http://dx.doi.org/10.1002/anie.202403667

    2. Bao, Y.; Jia, F.; Li, M.; Xu, R.; Xie, Y.; Zhang, F.*; Guo, J.* Characterizing the Molecular Mechanism of the Lethal C423D Mutation in FgMyoI: A Molecular Perspective. J Agric Food Chem 2024, 72, 1539-1549.  http://dx.doi.org/10.1021/acs.jafc.3c08648

    3. Li, M.; Zhang, X.; Li, S.; Guo, J.* Unraveling the Interplay of Extracellular Domain Conformational Changes and Parathyroid Hormone Type 1 Receptor Activation in Class B1 G Protein-Coupled Receptors: Integrating Enhanced Sampling Molecular Dynamics Simulations and Markov State Models. ACS Chem Neurosci 2024, 15, 844-853. http://dx.doi.org/10.1021/acschemneuro.3c00747

    4. Jiao, F.; Cui, W.; Wang, P.; Tong, H. H. Y.; Guo, J.*; Tao, J.* Synergistic inhibition mechanism of quinazolinone and piperacillin on penicillin-binding protein 2a: a promising approach for combating methicillin-resistant Staphylococcus aureus. J Biomol Struct Dyn 2024, 1-13. http://dx.doi.org/10.1080/07391102.2024.2330708

    5. Bao, Y.; Jia, F.; Li, M.; Xu, R.; Xie, Y.; Zhang, F.*; Guo, J.* Characterizing the Molecular Mechanism of the Lethal C423D Mutation in FgMyoI: A Molecular Perspective. J Agric Food Chem 2024, 72, 1539-1549.  http://dx.doi.org/10.1021/acs.jafc.3c08648

    6. Xu, R.; Bao, Y.; Jiao, F.; Li, M.; Zhang, X.; Zhang, F.*; Guo, J.* Unraveling the atomic mechanisms underlying glyphosate insensitivity in EPSPS: implications of distal mutations. J Biomol Struct Dyn 2024, 1-12.            http://dx.doi.org/10.1080/07391102.2024.2318472

    7. Guo, J*; Bao, Y; Li, M; Li, S; Xi, L; Xin, P; Wu, L; Liu, H; Mu, Y. Application of computational approaches in biomembranes: From structure to function. Wiley Interdiscip. Rev. Comput. Mol. Sci., 2023, 13, e1679.

    8. Xin, P.*; Xu, L.; Dong, W.; Mao, L.; Guo, J.*; Bi, J.; Zhang, S.; Pei, Y.; Chen, C. P.*, Synthetic K(+) Channels Constructed by Rebuilding the Core Modules of Natural K(+) Channels in an Artificial System. Angew. Chem. Int. Ed. Engl., 2023, 62, e202217859.
    9. M. Li; Y. Bao; Xu, R.; Li, M.; Xi, L.*; Guo, J.*, Understanding the Allosteric Modulation of PTH1R by a Negative Allosteric Modulator. Cells, 2023, 12, 41.
    10. Xu, R.; Bao, Y.; Li, M.; Zhang, Y.; Xi, L.; Guo, J.*, Computational Insights into the Allosteric Modulation of a Phthalate-Degrading Hydrolase by Distal Mutations. Biomolecules 2023, 13, 443.
    11. Bao, Y; Xu, Y; Jia, F; Li, M; Xu, R; Zhang, F*; Guo, J*. Allosteric inhibition of myosin by phenamacril: a synergistic mechanism revealed by computational and experimental approaches. Pest Manag. Sci. 2023, 79, 4977.
    12. Xi, L*; Shi, A; Shen, T; Wang, G; Wei, Y; Guo, J*. Licraside as novel potent FXR agonist for relieving cholestasis: structure-based drug discovery and biological evaluation studies. Front. in Pharmacol. 2023, 14, 1197856.
    13. Li, M.; Bao, Y.; Li, M.; Guo, J.*, GPCR Allostery: A View from Computational Biology. Curr. Med. Chem. 2023, 30, 4533.
    14. Li, M.;  Li, M.; Guo, J.*, Molecular Mechanism of Ca(2+) in the Allosteric Regulation of Human Parathyroid Hormone Receptor-1. J. Chem. Inf. Model. 2022, 62, 5110-5119.
    15. Li, M.; Bao, Y.; Xu, R.; Zhang, X.; La, H.; Guo, J.*, Mechanism of enhanced sensitivity of mutated beta-adrenergic-like octopamine receptor to amitraz in honeybee Apis mellifera: An insight from MD simulations. Pest Manag. Sci. 2022, 78, 5423.
    16. Li, M.; Bao, Y.; Xu, R.; La, H.; Guo, J.*, Critical Extracellular Ca2+ Dependence of the Binding between PTH1R and a G-Protein Peptide Revealed by MD Simulations. ACS Chem. Neurosci. 2022, 13, 1666-1674.
    17. Li, M.; Li, M.; Xie, Y.; Guo, J.*, Uncovering the Molecular Basis for the Better Gefitinib Sensitivity of EGFR with Complex Mutations over Single Rare Mutation: Insights from Molecular Simulations. Molecules 2022, 27 (12), 3844.
    18. Bao, Y.; Li, M.; Xie, Y.; Guo, J.*, Investigating the Permeation Mechanism of Typical Phthalic Acid Esters (PAEs) and Membrane Response Using Molecular Dynamics Simulations. Membranes 2022, 12 (6), 596.
    19. Li, M.; Xu, Y.; Guo, J.*, Insights into the negative regulation of EGFR upon the binding of an allosteric inhibitor. Chem. Biol. Drug. Des. 2022, 99 (4), 650-661.
    20. Li, M.; Guo, J.*, Deciphering the T790M/L858R-selective inhibition mechanism of an allosteric inhibitor of EGFR: insights from molecular simulations. ACS Chem. Neurosci. 2021, 12 (3), 462-472.
    21. Guo, J.*; Li, M.; Zhang, Y.; Xi, L.; Cui, F., Conformational dynamics is critical for the allosteric inhibition of cGAS upon acetyl-mimic mutations. Phys. Chem. Chem. Phys. 2021, 23 (3), 2154-2165.
    22. Guo, J.; Chia, G. W. N.; Berezhnoy, N. V.; Cazenave-Gassiot, A.;  Kjelleberg, S.;  Hinks, J.;  Mu, Y.*; Seviour, T.*, Bacterial lipopolysaccharide core structures mediate effects of butanol ingress. BBA-Biomembranes 2020, 1862, 183150.
    23. Zhong, W.#; Guo, J.#; Cui, L.#; Chionh, Y. H.; Li, K.; El Sahili, A.; Cai, Q.; Yuan, M.; Michels, P. A. M.; Fothergill-Gilmore, L. A.; Walkinshaw, M. D.; Mu, Y.*; Lescar, J.*; Dedon, P. C.*, Pyruvate kinase regulates the pentose-phosphate pathway in response to hypoxia in Mycobacterium tuberculosis. J. Mol. Biol. 2019, 431, 3690-3705.
    24. Guo, J.*; Wang, J.; Fan, J.; Zhang, Y.; Dong, W.; Chen, C. P.*, Distinct dynamic and conformational features of human STING in response to 2'3'-cGAMP and c-di-GMP. ChemBioChem 2019, 20, 1838-1847.
    25. Guo, J.; Ho, J. C. S.; Chin, H.; Mark, A. E.; Zhou, C.; Kjelleberg, S.; Liedberg, B.; Parikh, A. N.; Cho, N. J.; Hinks, J.; Mu, Y.*; Seviour, T.*, Response of microbial membranes to butanol: interdigitation vs. disorder. Phys. Chem. Chem. Phys. 2019, 21, 11903-11915.
    26. J. Guo; H. X. Zhou, Allosteric activation of SENP1 by SUMO1 beta-grasp domain involves a dock-and-coalesce mechanism. Elife, 2016, 5, e18249.
    27. J. Guo; H.-X. Zhou, Protein allostery and conformational dynamics. Chem. Rev., 2016, 116, 6503.
    28. J. Guo; X. Pang; H.-X. Zhou, Two pathways mediate interdomain allosteric regulation in pin1. Structure, 2015, 23, 237.

2025 Fall Ph.D. students recruiting

Our research group was established in 2022 and is affiliated with the Artificial Intelligence Drug Discovery Center at Macau Polytechnic University. With a focus on "IT+BT," our research primarily revolves around AI-based protein and drug design, integrating information technology and biotechnology to advance life science research through molecular modeling, artificial intelligence, and big data technologies.

Professor Guo Jingjing's research group welcomes students or scholars who are passionate about research and possess a team spirit to join us. We welcome students who are interested in protein engineering and design, computer-aided drug design, artificial intelligence drug design, bioinformatics, and related fields to join our research team and contribute to the deep integration of "IT" and "BT."

There are several positions available for master and Ph.D. students. We welcome applications!

Interested individuals are requested to send their resumes and contact information to: jguo@mpu.edu.mo.


Macao SAR Government Portal | News

Research Achievements in Biomembrane Studies by Scholars from Macao Polytechnic University Published in Top Computational Mathematics Journal

https://www.gov.mo/en/news/312819/

8th September 2023 at 15:52


DOI: https://doi.org/10.1002/wcms.1679

Journal of Hazardous Materials | Volume 475, 15 August 2024, 134828


Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction

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Highlights

  • Developed predictive models for bee toxicity and compound degradability, and revealed novel insights into their relationship.

  • The proposed model integrates pretraining, graph neural networks, and autoencoders for enhanced ecological impact prediction.


https://doi.org/10.1016/j.jhazmat.2024.134828