Research Projects
Discovery of novel drugs from natural bioactive products


Programme(s) to which this project applies:
☑ MPhil/PhD ☒ MRes[Med] ☒ URIS

Summary: This project will integrate meta-omics and machine learning to uncover yet unidentified bioactive compounds from marine sponges. These organisms are among the most prolific sources of marine natural products and provide a chemically diverse reservoir of compounds with important biological activities.

Objectives: 

  1. Use metagenomics and metabolomics to profile sponge microbiomes and metabolites and link metabolites to their producers.
  2. Apply an LLM-based workflow to identify sponge-derived compounds with antibiotic potential.
  3. Validate antibiotic candidates in vitro and isolate their microbial producers using high-throughput culturomics.


Research Questions

  1. Are sponge-derived natural products produced by the host or its symbionts?
  2. Can AI annotate untargeted metabolomics data and identify new antibacterial candidates?
  3. Do sponge-derived antibacterial candidates show selective, potent activity in vitro, and can they be produced sustainably?


Expected Outcomes: This project will discover new antibiotic candidates from deep-sea glass sponges by integrating meta-omics approaches (metabolomics, metagenomics and culturomics), AI-based modelling and bioactivity testing.

Dr S Zhang, Department of Pharmacology and Pharmacy

Dr. Shan Zhang is a microbiologist and bioinformatician. She obtained her Ph.D. in Microbiology and Immunology from the School of Biotechnology and Biomolecular Sciences at the University of New South Wales (UNSW), Sydney, Australia, in 2022. During her Ph.D. program, she visited the Medical Systems Biology Lab at Christian-Albrechts-University in Kiel, Germany, in 2019 as a visiting scholar. After completing her Ph.D. degree, she pursued postdoctoral fellowships at UNSW (from March 2022 to July 2023) and at HKUST (from August 2024 to March 2025). In March 2025, she joined the Department of Pharmacology and Pharmacy, LKS Faculty of Medicine at the University of Hong Kong (HKU), as a Research Assistant Professor.

During her Ph.D. program and postdoctoral research, her projects focused on the evolutionary adaptation of microbial symbionts to a symbiotic lifestyle, particularly through the integration of multi-omics approaches (e.g., metagenomics and metabolomics) to study sponges, the common ancestor of all animals, which allows to identify ancestral and conserved features in animal host-microbiome symbioses. Her expertise in cutting-edge bioinformatics techniques, such as genome-scale metabolic modeling, facilitates the exploration of metabolic interactions within host-microbiome symbioses. Additionally, she excels in integrating both culture-independent and culture-dependent approaches to investigate these topics and applies them to various host systems, ranging from animals (e.g., human, sponges and corals) to plants (e.g., seaweeds, wheat and tea).

After joining the Department of Pharmacology and Pharmacy, Dr. Zhang’s research has focused on the symbiotic relationships between the host gut and its associated eukaryotic (fungi) and prokaryotic microorganisms (bacteria and archaea), aiming to better understand host health and microbial physiology. 

Biography
ORCID
shanbio@hku.hk

For more information or to express interest for this project, please email the supervisor or the specified contact point in the project description.  Interested candidates are advised to enclose with your email:

  1. your CV,
  2. a brief description of your research interest and experience, and
  3. two reference letters (not required for HKUMed UG students seeking MRes[Med]/URIS projects).

Information on the research programme, funding support and admission documentations could be referenced online at the Research Postgraduate Admissions website. General admission enquiries should be directed to rpgmed@hku.hk.

HKUMed MBBS students interested in the Master of Research in Medicine (MRes[Med]) programme may visit the programme website for more information.  

HKUMed UG students interested in the Undergraduate Research Internship Scheme (URIS) may visit the scheme’s website for more information. 

Research @ Department of Pharmacology and Pharmacy