Page 13 - Undergraduate Research Opportunities Program Proceedings 2017-18

School of Science
Department of Chemistry

blueberries from 5 different brands are tested for setting up and validating the models. The result is found to be
relatively unreliable. Possible reasons and improvement are discussed.

Modeling Protein-ligand Interactions Using Docking and Other Computational Tools

Supervisor: HUANG Xuhui / CHEM
Student: CHAK Man Him / CHEM Course: UROP1100, Fall

Uncoupling proteins are responsible for proton leak in mammals. This is important for thermogenesis and reducing
oxidative stress in organisms. Recent studies have shown that the inhibition of UCP2 could lead to a relieve in
syndromes of Type 2 diabetes. However, natural purine inhibitors are too non-polar for aqueous cytosol environment
while genipin possess the undesirable cross-linking ability which may interfere with other biomolecules. Therefore in this
report, the binding pattern of genipin are analysed using Autodock Vina and other computational tools in light to
modify and come up with better alternatives of genipin.

Supervisor: HUANG Xuhui / CHEM
Student: CHOY Ka Hei / CBME Course: UROP1100, Summer

In the project, we will firstly introduce the concepts of classical mechanics such as formulation of Hamiltonian mechanics,
Liouville Theorem and its equations which is crucial for developing the MSMs. Then, I will review basic principle of MSMs
describing stochastic dynamics of a biomolecular system aiming to elucidate large scale conformational changes of the
system via computational stimulations with high resolution of space and time that is beneficial for understanding the
corresponding biological work of the investigated molecule. Finally, we will discuss the applications of MSMs such as
transcription process of RNA Polymerase II and colloidal assembly process control.

Mechanisms of Influenza A virus Replication and Implication to New Drug Discoveries

Supervisor: HUANG Xuhui / CHEM Co-Supervisor CHEUNG Pak Hang Peter / CHEM
Student: HAN Jeewon / CHEM Course: UROP1100, Fall

Influenza A virus (IAV) is a notorious pandemic virus that has a high mortality in humans. Viral RNA in IAV is transcribed
and replicated by RNA-dependent RNA polymerase (RdRp) in eukaryotes. Although exact pathways of RNA transcription,
replication, and spread are still obscure, blocking entry and exit channels of the active site may cause the polymerase
stop functioning and thus prevent viral genome from spreading. The aim of this project is to provide an insight on
developing antiviral drugs by researching the RNA synthesis to validate ways to inhibit RdRp from transcribing and
replicating viral genome. I will first review steps of IAV replication, leading to plans of this project, and show preliminary
results.

Supervisor: HUANG Xuhui / CHEM Co-Supervisor CHEUNG Pak Hang Peter / CHEM
Student: KEI Hoi Shan / CHEM Course: UROP1000, Summer

Influenza A virus (IAV) is in Orthomyxoviridae family, IAV infect respiratory system of human body and can always cause
pandemics, like H1N1 (swine flu), H2N1 (Asian flu). Invention of drugs for inhibiting the virus is important for decreasing
number of deaths in the pandemics. In order to design effective drug, we need to have deeper understanding on the
structure of influenza A virus and the mechanism that it replicates in human body. This report will introduce the

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