Tâp HA DUONG 

Professor

Molecular Modeling

Deputy Director of the ITFA Doctoral School, Head of Training Programs



Fluorinated Molecules, Permanent


bureau
tap.ha-duong@universite-paris-saclay.fr


0180006376

HM1- 1er étage - 1804


ORCID
https://orcid.org/0000-0002-0847-2948


Enseignement


    

  • Bases et principes de la conception in silico de molécules thérapeutiques (3e année de Pharmacie, L3 interface Biologie-Chimie)
    • 



    

  • Stratégies et outils in silico de découverte et développement de médicaments (4e année de Pharmacie, M1 Sciences du Médicament)
    • 



    

  • Bioinformatics, biomolecular modeling, and drug design (M2 Chimie Thérapeutique, M2 Development of Drugs and Health Products)
    • 



    

  • Responsable de l’UE Chimie Médicinale en L3 iBC et de de l’UE Biomolecular Modeling and Bioinformatics en M2 D2HP
    • 



    

  • Co-responsable de l’UE Initiation à la Découverte de Médicaments en M1 Sciences du Médicament
    • 



Recherche


    

  • Modeling protein structural ensembles and protein-ligand interactions
    • 



    

  • Simulations of biomolecular condensates and polymeric nanoparticles
    • 



    

  • Design of peptide-derived inhibitors of protein-protein interactions
    • 



    

  • Deep-learning approaches to model biomolecules and their complexes
    • 



    

  • Coordinator of the molecular modeling group
    • 

























39 documents







Journal articles36 document




    

  • Ping Gao, Xin Jiang, Jinyu Li, Julien Nicolas, Tâp Ha-Duong. Molecular Simulations of Polymer‐based Drug Nanocarriers: From Physical and Structural Properties to Controlled Release. Advanced Healthcare Materials, 2026, pp.e03503. ⟨10.1002/adhm.202503503⟩. ⟨hal-05459572⟩
    • 

  • Tran Ngoc Anh Nguyen, Hong-Toan Lai, Romain Fernandes, Filippo G Dall’olio, Camille Blériot, et al.. Apoptosis-inducing factor (AIF) at the crossroad of cell survival and cell death: implications for cancer and mitochondrial diseases. Cell Communication and Signaling, 2025, 23, ⟨10.1186/s12964-025-02272-2⟩. ⟨hal-05217821⟩
    • 

  • Yingmin Jiang, Tâp Ha-Duong. Temperature-Dependent Coarse-Grained Model for Simulations of Intrinsically Disordered Protein LCST and UCST Liquid–Liquid Phase Separations. Journal of Chemical Theory and Computation, 2025, 21 (9), pp.4939-4952. ⟨10.1021/acs.jctc.5c00212⟩. ⟨hal-05373622⟩
    • 

  • Ning Liu, Ping Gao, Hai-Yan Lu, Lei Fang, Julien Nicolas, et al.. Polyfluoroalkyl Chain‐Based Assemblies for Biomimetic Catalysis. Chemistry - A European Journal, In press, 30 (1), ⟨10.1002/chem.202302669⟩. ⟨hal-04252759⟩
    • 

  • José Laxio Arenas, Jacopo Lesma, Tap Ha‐duong, Bikash Ranjan Sahoo, Ayyalusamy Ramamoorthy, et al.. Composition and Conformation of Hetero‐ versus Homo‐Fluorinated Triazolamers Influence their Activity on Islet Amyloid Polypeptide Aggregation. Chemistry - A European Journal, 2024, 30 (28), pp.e202303887. ⟨10.1002/chem.202303887⟩. ⟨hal-04756674⟩
    • 

  • Ping Gao, Tâp Ha-Duong, Julien Nicolas. Coarse‐Grained Model‐Assisted Design of Polymer Prodrug Nanoparticles with Enhanced Cytotoxicity: A Combined Theoretical and Experimental Study. Angewandte Chemie, 2024, ⟨10.1002/ange.202316056⟩. ⟨hal-04468750⟩
    • 

  • Camille Lozada, Simon Gonzalez, Rémy Agniel, Mathilde Hindie, Luca Manciocchi, et al.. Introduction of constrained Trp analogs in RW9 modulates structure and partition in membrane models. Bioorganic Chemistry, 2023, 139, pp.106731. ⟨10.1016/j.bioorg.2023.106731⟩. ⟨hal-04272386⟩
    • 

  • Chenghui Shi, Julia Kaffy, Tâp Ha-Duong, Jean-François Gallard, Alain Pruvost, et al.. Proteolytically Stable Diaza-Peptide Foldamers Mimic Helical Hot Spots of Protein–Protein Interactions and Act as Natural Chaperones. Journal of Medicinal Chemistry, 2023, 66 (17), pp.12005-12017. ⟨10.1021/acs.jmedchem.3c00611⟩. ⟨hal-04458911⟩
    • 

  • Liuba Mazzanti, Tâp Ha-Duong. Understanding Passive Membrane Permeation of Peptides: Physical Models and Sampling Methods Compared. International Journal of Molecular Sciences, 2023, 24 (5), pp.5021. ⟨10.3390/ijms24055021⟩. ⟨hal-05375544⟩
    • 

  • Ping Gao, Julien Nicolas, Tâp Ha-Duong. Supramolecular Organization of Polymer Prodrug Nanoparticles Revealed by Coarse-Grained Simulations. Journal of the American Chemical Society, 2021, 143 (42), pp.17412-17423. ⟨10.1021/jacs.1c05332⟩. ⟨hal-03805438⟩
    • 

  • Jacopo Lesma, Faustine Bizet, Corentin Berardet, Nicolo Tonali, Sara Pellegrino, et al.. β-Hairpin Peptide Mimics Decrease Human Islet Amyloid Polypeptide (hIAPP) Aggregation. Frontiers in Cell and Developmental Biology, 2021, 9, ⟨10.3389/fcell.2021.729001⟩. ⟨hal-03367992⟩
    • 

  • Anne-Elisabeth Molza, Ping Gao, Justine Jakpou, Julien Nicolas, Nicolas Tsapis, et al.. Simulations of the upper critical solution temperature behavior of poly(ornithine-co-citrulline)s using Martini-based coarse-grained force fields. Journal of Chemical Theory and Computation, 2021, 17 (7), pp.4499-4511. ⟨10.1021/acs.jctc.1c00140⟩. ⟨hal-03286381⟩
    • 

  • José Laxio Arenas, Yaochun Xu, Thierry Milcent, Carine van Heijenoort, Francois Giraud, et al.. Fluorinated Triazole Foldamers: folded or extended conformational preferences. ChemPlusChem, 2021, ⟨10.1002/cplu.202000791⟩. ⟨hal-03796604⟩
    • 

  • Maud Chan-Yao-Chong, Stéphanie Marsin, Sophie Quevillon-Cheruel, Dominique Durand, Tâp Ha-Duong. Structural ensemble and biological activity of DciA intrinsically disordered region. Journal of Structural Biology, 2020, pp.107573. ⟨10.1016/j.jsb.2020.107573⟩. ⟨hal-02903062⟩
    • 

  • Sébastien Pomel, Wei Mao, Tâp Ha-Duong, Christian Cavé, Philippe Loiseau. GDP-Mannose Pyrophosphorylase: A Biologically Validated Target for Drug Development Against Leishmaniasis. Frontiers in Cellular and Infection Microbiology, 2019, 9, ⟨10.3389/fcimb.2019.00186⟩. ⟨hal-05149150⟩
    • 

  • Maud Chan-Yao-Chong, Celia Deville, Louise Pinet, Carine Van Heijenoort, Dominique Durand, et al.. Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data. Biophysical Journal, 2019, 116 (7), pp.1216--1227. ⟨10.1016/j.bpj.2019.02.015⟩. ⟨hal-02169943⟩
    • 

  • Maud Chan-Yao-Chong, Dominique Durand, Tâp Ha-Duong. Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles. Journal of Chemical Information and Modeling, 2019, 59 (5), pp.1743--1758. ⟨10.1021/acs.jcim.8b00928⟩. ⟨hal-02169939⟩
    • 

  • Maud Chan-Yao-Chong, Dominique Durand, Tâp Ha-Duong. Investigation into Early Steps of Actin Recognition by the Intrinsically Disordered N-WASP Domain V. International Journal of Molecular Sciences, 2019, 20 (18), pp.4493. ⟨10.3390/ijms20184493⟩. ⟨hal-02294231⟩
    • 

  • Nicolo Tonali, Julia Kaffy, Jean-Louis Soulier, Maria Luisa Gelmi, Emanuela Erba, et al.. Structure-activity relationships of β-hairpin mimics as modulators of amyloid β-peptide aggregation. European Journal of Medicinal Chemistry, 2018, 154, pp.280-293. ⟨10.1016/j.ejmech.2018.05.018⟩. ⟨hal-04305545⟩
    • 

  • Nicolo Tonali, Julia Kaffy, Jean-Louis Soulier, Maria Luisa Gelmi, Emanuela Erba, et al.. Structure-activity relationships of β-hairpin mimics as modulators of amyloid β-peptide aggregation. European Journal of Medicinal Chemistry, 2018, 154, pp.280-293. ⟨10.1016/j.ejmech.2018.05.018⟩. ⟨hal-02392954⟩
    • 

  • Florian Malard, Nadine Assrir, Mouad Alami, Samir Messaoudi, Ewen Lescop, et al.. Conformational Ensemble and Biological Role of the TCTP Intrinsically Disordered Region: Influence of Calcium and Phosphorylation. Journal of Molecular Biology, 2018, 430 (11), pp.1621-1639. ⟨10.1016/j.jmb.2018.04.024⟩. ⟨hal-02114798⟩
    • 

  • Yaochun Xu, Isabelle Correia, Tap Ha-Duong, Nadjib Kihal, Jean-Louis Soulier, et al.. The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands. Beilstein Journal of Organic Chemistry, 2017, 13, pp.2842 - 2853. ⟨10.3762/bjoc.13.276⟩. ⟨hal-01700974⟩
    • 

  • Pasquale Cutolo, Nathalie Basdevant, Guillaume Bernadat, Françoise Bachelerie, Tâp Ha-Duong. Interaction of chemokine receptor CXCR4 in monomeric and dimeric state with its endogenous ligand CXCL12: coarse-grained simulations identify differences. Journal of Biomolecular Structure and Dynamics, 2017, 35 (2), pp.399-412. ⟨10.1080/07391102.2016.1145142⟩. ⟨hal-02110176⟩
    • 

  • Wei Mao, Pierre Daligaux, Noureddine Lazar, Tâp Ha-Duong, Christian Cavé, et al.. Biochemical analysis of leishmanial and human GDP-Mannose Pyrophosphorylases and selection of inhibitors as new leads. Scientific Reports, 2017, 7, pp.751. ⟨10.1038/s41598-017-00848-8⟩. ⟨hal-02390042⟩
    • 

  • Linh Tran, Nathalie Basdevant, C Prévost, Tâp Ha-Duong. Structure of ring-shaped Aβ42 oligomers determined by conformational selection. Scientific Reports, 2016, 6, pp.21429. ⟨10.1038/srep21429⟩. ⟨hal-01497983⟩
    • 

  • Pierre Daligaux, Guillaume Bernadat, Linh Tran, Christian Cavé, Philippe Loiseau, et al.. Comparative study of structural models of Leishmania donovani and human GDP-mannose pyrophosphorylases. European Journal of Medicinal Chemistry, 2016, 107, pp.109-118. ⟨10.1016/j.ejmech.2015.10.037⟩. ⟨hal-05149041⟩
    • 

  • Carla Jamous, Nathalie Basdevant, Tap Ha-Duong. Influence of GTP/GDP and magnesium ion on the solvated structure of the protein FtsZ: a molecular dynamics study. Journal of Biomolecular Structure and Dynamics, 2014, 32 (6), pp.916-927. ⟨10.1080/07391102.2013.799436⟩. ⟨hal-02112312⟩
    • 

  • Nathalie Basdevant, Daniel Borgis, Tap Ha-Duong. Modeling Protein–Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION. Journal of Chemical Theory and Computation, 2013, 9 (1), pp.803-813. ⟨10.1021/CT300943W⟩. ⟨hal-02112584⟩
    • 

  • Amal Saidi Brikci-Nigassa, Marie-Jeanne Clément, Tâp Ha-Duong, Elisabeth Adjadj, Latifa Ziani, et al.. Phosphorylation Controls the Interaction of the Connexin43 C-Terminal Domain with Tubulin and Microtubules. Biochemistry, 2012, 51 (21), pp.4331-4342. ⟨10.1021/bi201806j⟩. ⟨hal-02292202⟩
    • 

  • Marie-Jeanne Clément, Boï-Trinh Kuoch, Tâp Ha-Duong, Vandana Joshi, Loic Hamon, et al.. The Stathmin-Derived I19L Peptide Interacts with FtsZ and Alters Its Bundling. Biochemistry, 2009, 48 (41), pp.9734-9744. ⟨10.1021/bi900556a⟩. ⟨hal-02295213⟩
    • 

  • Tap Ha-Duong, Nathalie Basdevant, Daniel Borgis. A polarizable coarse-grained water model for coarse-grained proteins simulations. Chemical Physics Letters, 2009, 468 (1-3), pp.79-82. ⟨10.1016/j.cplett.2008.11.092⟩. ⟨hal-04710697⟩
    • 

  • Nathalie Basdevant, Daniel Borgis, Tap Ha-Duong. A Coarse-Grained Protein−Protein Potential Derived from an All-Atom Force Field. Journal of Physical Chemistry B, 2007, 111 (31), pp.9390-9399. ⟨10.1021/jp0727190⟩. ⟨hal-04710687⟩
    • 

  • N. Basdevant, T. Ha-Duong, D. Borgis. Particle-based implicit solvent model for biosimulations : Application to proteins and nucleic acids hydration.. Journal of Chemical Theory and Computation, 2006, pp.1646-1656. ⟨hal-00158057⟩
    • 

  • Nathalie Basdevant, Tap Ha-Duong, Daniel Borgis. Dielectric constant of a highly polarizable atomic fluid: the clausius–mossotti versus the onsager relation. Molecular Physics, 2006, 102 (8), pp.783-788. ⟨10.1080/00268970410001711328⟩. ⟨hal-04710670⟩
    • 

  • Nathalie Basdevant, Daniel Borgis, Tap Ha-Duong. A semi‐implicit solvent model for the simulation of peptides and proteins. Journal of Computational Chemistry, 2004, 25 (8), pp.1015-1029. ⟨10.1002/jcc.20031⟩. ⟨hal-04710660⟩
    • 

  • T. Haduong, K. Zakrzewska. Influence of drug binding on DNA flexibility: a normal mode analysis.. Journal of Biomolecular Structure and Dynamics, 1997, 14, pp.691-701. ⟨hal-00314955⟩
    • 












Conference papers1 document




    

  • N. Basdevant, T. Ha-Duong, D. Borgis. A particle based implicit solvent model for biomolecular simulations. From Physics to Biology : The Interface between Experiment and Computation : BIFI 2006 II International Congress, Feb 2006, Zaragoza, Spain. ⟨hal-00159799⟩
    • 












Preprints, Working Papers2 document




    

  • José Laxio Arenas, Jacopo Lesma, Tap Ha-Duong, Bikash Sahoo, Ayyalusamy Ramamoorthy, et al.. Relation between conformation and activity on islet amyloid polypeptide aggregation of fluorinated foldamers based on Ndifluoromethyl-1,4-triazole amino acids. 2023. ⟨hal-04273096⟩
    • 

  • Marion Barthé, Flora Lefebvre, Emilie Langlois, Florence Lefebvre, Patrick Lechêne, et al.. PEGylated isoprenaline reveals distinct functions of cardiac β-adrenergic receptors located in the T-tubule vs . outer surface membrane. 2022. ⟨hal-03793970⟩
    • 
















Powered by HAL logo