Master’s Student Yuxin Xie Advances Computational Drug Discovery Research

The collaborative research team behind the HIV-1 protease inhibitor study (anti-clockwise from right):

Dr Faez Iqbal Khan, Master's student Yuxin Xie, PhD student Danwen Qiu, and Dr Magdalini Matziari.

Yuxin Xie is a Master's student in Biosciences and Bioinformatics at Xi'an Jiaotong-Liverpool University, working under the supervision of Dr Faez Iqbal Khan, whose research focuses on computational biology and structure-based drug discovery. During her studies, Yuxin has demonstrated exceptional dedication and research capability, resulting in three peer-reviewed publications in high-impact international journals.

In her first-author study, conducted in collaboration with Dr Magdalini Matziari and PhD student Danwen Qiu, Yuxin performed molecular dynamics and binding free energy analyses of phosphinate pseudopeptide inhibitors targeting HIV-1 protease. The work, titled “Phosphinate Pseudopeptide Enhances Binding Free Energy in HIV-1 Protease by Driving Flap Closure and Suppressing Global Flexibility,” provides atomic-level insights into inhibitor binding mechanisms and identifies promising lead compounds for antiviral development. The study has been accepted in Protein Science (Impact Factor: ~5.2, 2026). This project marked her first experience as a lead author in computational drug discovery, where she identified the impact of chiral isomers on inhibitory affinity and addressed the challenge of analysing subtle conformational changes within the binding pocket. This work strengthened her ability to interpret computational results through a biological lens.

In another collaborative project, she contributed to the design and computational evaluation of serine-derived phosphinic peptides as MMP-13 inhibitors. The study, titled “Novel Serine-Derived Phosphinic Peptides as Potent MMP-13 Inhibitors,” integrates docking, molecular dynamics simulations, and ADMET predictions to assess inhibitor potency and drug-likeness. Published in Bioorganic Chemistry (Impact Factor: ~4.7, 2026), the work highlights compounds with high-nanomolar inhibitory activity and provides direction for further therapeutic optimization. This study also underscored the importance of integrating pharmacokinetics and pharmacodynamics in drug design and offered valuable interdisciplinary collaboration experience with synthetic chemists.

Yuxin has also contributed to a multidisciplinary study with Prof. Hassan investigating the stability landscape of Aurora kinase B under guanidinium chloride-induced unfolding. The work, titled “Investigating Stability Landscape of Aurora Kinase B Probed by Guanidinium Chloride-Induced Unfolding,” combines spectroscopy and molecular dynamics simulations to elucidate the two-state unfolding mechanism and structural determinants of kinase stability. Published in International Journal of Biological Macromolecules (Impact Factor: ~8.5, 2026), this work further strengthened her problem-solving skills and deepened her understanding of how simulations complement experimental approaches, while enhancing her ability to work effectively in multidisciplinary teams.

With three publications in high-impact journals during her Master’s studies, Yuxin has made meaningful scientific contributions. She is recognised as a collaborative, methodical researcher who brings energy and commitment to every project.

Beyond her research achievements, Yuxin is a dedicated student who contributes positively to a supportive and collaborative research environment. Several additional co-authored manuscripts are currently in progress. She actively promotes team learning by sharing knowledge and developing practical tools, including a Python-based workflow for automated structural feature extraction and molecular visualisation, significantly improving group efficiency. Under Dr. Khan's supervision, Yuxin has thrived in a collaborative and intellectually stimulating research environment.

Content：Dr Faez Iqbal Khan
Review：Professor John Moraros、Dr Faez Iqbal Khan