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. Study on AChE inhibitory activity of compounds extracted from Neem seed essential oil using computational tools (AOTA International Joint Stock Company).
   Project Code: 05/AOTA-HĐKT (Completed: 2025).

2. Study on the effects of hydrophobic core mutations on the structure of Aβ protofibrils using replica-exchange molecular dynamics simulations (NAFOSTED).
   Project Code: 103.01-2016.48 (Completed: 2019).

3. Mechanism of Ca²⁺ ion transport through ion channel-like structures formed by transmembrane Aβ peptides: an in silico study.
   Project Code: 104.99-2019.57 (Completed: 2021).

4. Study on the structure and substrate selectivity of AA13 enzymes using quantum calculations and molecular simulations.
   Project Code: 103.01-2017.368 (Completed: 2019).

5. Research on polysaccharide monooxygenase enzymes and related enzymes in the pathogenicity of Magnaporthe oryzae and some applications.
   Project Code: NĐT.36.ITA/18 (Completed: 2021).

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

7. Research using computational simulations combined with experiments to search for potential anticancer compounds from naturally derived xanthone scaffolds (National Program 562).

8. Design, synthesis, and biological evaluation of novel multifunctional tetrazole derivatives for potential use in Alzheimer’s disease treatment (VinIF).
   Project Code: VINIF.2022.DA00061 (Completed: 2024).

Selected Publications:

	Hoang Anh Nguyen, Trung Hai Nguyen, Van V. Vu, Philippe Derreumaux and Son Tung Ngo. Varoglutamstat Inhibits the Dimerization of the Aβ25–35 Fragment in Aqueous Solution.The Journal of Physical Chemistry B (2025).
	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: 

	Tan M. Dang, Thi D. T. Nguyen, Tam V.-T. Mai, Son Tung Ngo and Lam K. Huynh (2025). Atmospheric Oxidation of N-Methyl Succinimide Initiated by OH Radicals: A Theoretical Study. ACS Earth and Space Chemistry.
	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)