The Laboratory of Theoretical Chemistry (LTC), founded by Ton Duc Thang University, is at the interface among biology, chemistry, physics, and computer science. Its objectives are to develop new simulation methods to predict physical properties of peptides and proteins in vitro or cellular environments, and to understand the molecular mechanisms responsible for Alzheimer’s disease.
2. Mission and vision
Alzheimer’s disease (AD) is affecting more than 50 millions of people worldwide and there is no effective drug thus far. It is believed that the small oligomers of the amyloid-beta (AD) protein of 39-43 amino acids are the main toxic species, although the formation of tangles made of the tau protein of 441 residues is the second hallmark of AD. Due to their transient characters, we do not have any structural information of all oligomers.
The main goal, based on computer simulations coupled when possible to experimental studies such as solid-state NMR, is to understand the self-assembly of AD and tau protein in aqueous solution, on the surface or in membrane bilayers. Interactions with important protein targets, possible drugs and the use of new technologies will also be considered.
The LTC aims at solving four main issues:
- Further develop Lattice Boltzmann Molecular dynamics simulations with coarse-grained models allowing large dimension-system and time scale of biological systems and of a coarse-grained model for lipids compatible with the OPEP protein model.
- Replica exchange MD simulations or simulated tempering simulations with atomistic or the coarse-grained OPEP protein model at different levels of resolution to understand the self-assembly of the AD and tau proteins in aqueous solution, near and within neuronal membrane.
- On-lattice replica-exchange and standard Monte Carlo simulations to understand the mesoscopic mechanisms underlying the aggregation of amyloids.
- Develop new technologies to open the blood-brain-barrier and allowing the delivery of drugs.
3. Research topics
- Amyloid aggregation simulations.
- Coarse-grained models for proteins and lipids.
- On-lattice and off-lattice replica exchange Monte Carlo and Molecular Dynamics simulations.
- Toxicity of amyloid aggregates made of the AD and tau proteins.
4. Current members
Prof. Philippe Derreumaux
Positions: Head of Laboratory of Theoretical Chemistry, Ton Duc Thang University, Viet Nam
Areas of expertise: Development of enhanced sampling approaches and force fields at a coarse grained level, protein structure prediction, computer simulations, amyloid aggregation and Alzheimer’s disease.
Research track record (9 January 2019):
• ISI papers: 101
• Total ISI Citations: 5542
• ISI H-index: 46
• Top ISI journals (at most 5):
1. Chemical Reviews (Impact factor: 52.6)
2. Chemical Society Reviews (Impact factor: 40.2)
3. Nucleic Acids Research (Impact factor: 11.6)
4. Account Chemical Research (Impact factor: 20.9)
5. Journal of the American Chemical Society (Impact Factor: 14.4)
Dr. Phuong H Nguyen
Position: Member of Laboratory of Laboratory of Theoretical Chemistry, Ton Duc Thang University, Viet Nam
Areas of expertise: Simulated tempering, non-equilibrium molecular dynamics simulations, impact of bubble cavitation and picosecond infrared laser on biological systems
5. Publications (ISI or Scopus only)
- Son Tung Ngo, Phuong H. Nguyen, and Philippe Derreumaux* (2020); Stability of Aβ11–40 Trimers with Parallel and Antiparallel β-Sheet Organizations in a Membrane-Mimicking Environment by Replica Exchange Molecular Dynamics Simulation; J. Phys. Chem. B (ISI).
- Son Tung Ngo, Phuong H. Nguyen, and Philippe Derreumaux* (2020); Impact of A2T and D23N Mutations on Tetrameric Aβ42 Barrel within a Dipalmitoylphosphatidylcholine Lipid Bilayer Membrane by Replica Exchange Molecular Dynamics; J. Phys. Chem. B (ISI).
- Philippe Derreumaux*, Viet Hoang Man, Junmei Wang, and Phuong H. Nguyen (2020); Tau R3–R4 Domain Dimer of the Wild Type and Phosphorylated Ser356 Sequences. I. In Solution by Atomistic Simulations; J. Phys. Chem. B(ISI).
- Phuong H.Nguyen, PhilippeDerreumaux (2020); Structures of the intrinsically disordered Aβ, tau and α-synuclein proteins in aqueous solution from computer simulations; Biophysical Chemistry (ISI).
- Huynh Minh Hung, Minh Tho Nguyen, Phuong-Thao Tran, Vi Khanh Truong, James Chapman, Le Huu Quynh Anh, Philippe Derreumaux, Van V. Vu and Son Tung Ngo* (2020); Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ40 Peptide; Journal of Chemical Information and Modeling (ISI).
- Phuong H. Nguyen, Josep M. Campanera, Son Tung Ngo, Antoine Loquet, Philippe Derreumaux* (2019); Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution; ACS Publications (ISI).
- Viet Hoang Man, Mai Suan Li, Junmei Wang, Philippe Derreumaux and Phuong H. Nguyen (2019); Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion; The Journal of Chemical Physics (ISI).
- Fernando Luís Barroso da Silva, Fabio Sterpone and Philippe Derreumaux* (2019); OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field; ACS Publications (ISI).
- Phuong H. Nguyen, Josep M. Campanera, Son Tung Ngo, Antoine Loquet and Philippe Derreumaux (2019); Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane; ACS Publications (ISI).
- Yan Lu, Xiao-Feng Shi, Phuong H. Nguyen, Fabio Sterpone, Freddie R. Salsbury and Philippe Derreumaux (2019); Amyloid-β(29–42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids; ACS Publications (ISI).
- Viet Hoang Man, Phan Minh Truong, Mai Suan Li, Junmei Wang, Nguyen-Thi Van-Oanh, Philippe Derreumaux and Phuong H. Nguyen (2018); Molecular Mechanism of the Cell Membrane Pore Formation Induced by Bubble Stable Cavitation ; ACS Publications (ISI).
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