Research Laboratory of Biophysics

Main Research Direction

The research focuses on the structure, function, and interactions of biologically important molecules such as proteins, genes, and cell membranes. The aim is to design compounds targeting key molecules such as the Amyloid beta peptide, neuraminidase, Mpro of the SARS-CoV-2 virus, etc. This work also includes the development and improvement of computational methods to model and simulate biological systems, as well as software for predicting biochemical processes.

Members of the Strong Research Group

Current scientific tasks:

1. Researching compounds that inhibit AChE to aid in the treatment of dementia using a combination of machine learning (ML) models, molecular dynamics simulations, and in vitro testing (Ho Chi Minh City Department of Science and Technology).

2. Searching for compounds with strong inhibition of the Covid-19 virus from Phyllanthus acidus (star gooseberry) and Phyllanthus emblica (Indian gooseberry) (NAFOSTED).

Completed scientific tasks:

1. Research on the AChE inhibitory activity of compounds extracted from Neem seed oil using computational tools (AOTA International Joint Stock Company).

2. Studying the impact of mutations in the hydrophobic core region on the structure of Aβ protofibrils using molecular dynamics simulations with model exchange (NAFOSTED).

3. Mechanism of Ca²⁺ ion movement through ion channel-like structures formed by Aβ peptides: in silico study.

4. Study of the structure and substrate specificity of AA13 enzymes using quantum calculations and molecular simulations.

5. Study of polysaccharide monooxygenase enzymes and related enzymes in the pathogenic process of the fungus Magnaporthe oryzae and some applications.

6. Study of the geometric structure, electronic structure, energy parameters, and physical properties of aluminum-based atomic systems at the nanoscale doped with various transition metals.

7. Study using computational simulation combined with experimental methods to search for potential anticancer compounds from natural xanthone-based compounds (State Project 562).

8. Design, synthesis, and evaluation of the biological activity of new multifunctional tetrazole derivatives for the treatment of Alzheimer’s disease (VinIF).

Selected Publications:

	Quynh Mai Thai, Nguyen Thanh Tung, Dung Do Thi Mai, Son Tung Ngo, Dimerization of the Aβ42 under the Influence of the Gold Nanoparticle: A REMD Study. J. Phys. Chem. B 2024, 128, 47, 11705–11713. (Q1, IF: 2.8)
	Thi-Kim-Dung Le, Thuc-Huy Duong, Warinthorn Chavasiri. Chemical constituents with their alpha-glucosidase inhibitory activity from the whole plant of Ceratophyllum demersum. Phytochemistry. 2025, 229,  114290 (Q1, IF: 3.2)
	Phuong Nguyen, Ayyalusamy Ramamoorthy, Bikash Sahoo, Jie Zheng, Peter Faller, John Straub, Laura Domínguez, Joan-Emma Shea, Nikolay Dokholyan, Alfonso De Simone, Buyong Ma, Ruth Nussinov, Saeed Najafi, Son Tung Ngo, Antoine Loquet, Mara Chiricotto, Pritam Ganguly, James McCarty, Mai Suan Li, Carol Hall, Yiming Wang, Yifat Miller, Simone Melchionna, Birgit Habenstein, Stepan Timr, Jiaxing Chen, Brianna Hnath, Birgit Strodel, Rakez Kayed, Sylvain Lesne, Guanghong Wei, Fabio Sterpone, Andrew Doig, Philippe Derreumaux, Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes and Amyotrophic Lateral Sclerosis. Chem. Rev. 2021, 121, 2545–2647. (Q1, IF: 51.5)

New publication: 

	Quynh Mai Thai, Trung Hai Nguyen, George Binh Lenon, Huong Thi Thu Phung, Jim-Tong Horng, Phuong-Thao Tran, Son Tung Ngo. Estimating AChE inhibitors from MCE database by machine learning and atomistic calculations. J. Mol. Graph. Model. 2025, 134, 108906. (Q2, IF: 2.7)
	Pham Thi Thu Thao, Dinh Quy Huong, Nguyen Minh Thong, Mai Van Bay, Son Tung Ngo, Quan Van Vo, Pham Cam Nam. Revisiting the radical trapping activity of N–H and O–H in N-phenylhydroxylamine: a DFT study. Phys. Chem. Chem. Phys. 2025, 27, 8457-8466 (Q2, IF: 3.7)
	Tran Thi Hoai Van, Minh Quan Pham, Truong Thi Thu Huong, Bui Nguyen Thanh Long, Pham Quoc Long, Le Thi Thuy Huong, George Binh Lenon, Nguyen Thi Thanh Uyen, Son Tung Ngo. Searching potential GSK-3β inhibitors from marine sources using atomistic simulations. Mol. Divers. 2025 (Q2, IF: 3.9)
	Quynh Mai Thai, Huong TT Phung, Nguyen Thanh Tung, Linh Hoang Tran, Son Tung Ngo. Assessing the ligand-binding affinity of chitinase inhibitors using steered-molecular simulations. Chem. Phys. Lett. 2025, 864, 141899. (Q2, IF: 2.8)
	Thong Nguyen-Minh Le, Thong Le Minh Pham, Thang Bach Phan, Yoshiyuki Kawazoe. Stabilization of small organic molecules on V2C and V2CO2 MXenes: first-principles insights into the performance of van der Waals functionals and the effect of oxygen vacancies. RSC Adv. 2025, 15, 301-311. (Q1, IF: 3.9)