Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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Inhibitors, protein aggregation and carbon nanotube

2011/01/B/NZ1/01622

Keywords:

inhibitors protein aggregation amino acids peptides amyloid Alzheimer's disease all-atom simulations docking method

Descriptors:

  • NZ1_3:
  • NZ1_1:
  • ST4_15:

Panel:

NZ1 - Molecular biology, structural biology, biotechnology: molecular biology, structural biology, biotechnology

Host institution :

Instytut Fizyki Polskiej Akademii Nauk

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Mai Suan Li 

Number of co-investigators in the project: 5

Call: OPUS 1 - announced on 2011-03-15

Amount awarded: 214 500 PLN

Project start date (Y-m-d): 2011-12-06

Project end date (Y-m-d): 2014-12-05

Project duration:: 36 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Serwer obliczeniowy (60 000 PLN)
  2. Notebook (3 000 PLN)
  3. Oprogramowanie (5 szt.) (3 298 PLN)

Information in the final report

  • Publication in academic press/journals (38)
  1. In silico and in vitro characterization of anti-amyloidogenic activity of vitamin K3 analogues for Alzheimer's disease
    Authors:
    P.D.Q. Huy, Y-C. Yu, Son Tung Ngo, Tran Van Thao, C-P Chen, M. S. Li, and Y-C Chen
    Academic press:
    Biochimica et Biophysica Acta-General Subjects (rok: 2013, tom: 1380, strony: 2960-2969), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bbagen.2012.12.026 - link to the publication
  2. Exploring the potent inhibitors against NS3/4A protease of hepatitis C virus using steered molecular dynamics technique
    Authors:
    Arthitaya Meeprasert, Thanyada Rungrotmongkol, Mai Suan Li, Supot Hannongbua
    Academic press:
    Current Pharmaceutical Design (rok: 2014, tom: 20, strony: 3465), Wydawca: BENTHAM SCIENCE PUBL LTD
    Status:
    Published
  3. Amyloid oligomer structure characterization from simulations: A general method
    Authors:
    Phuong Hoang Nguyen, Philippe Derreumaux, and Mai Suan Li
    Academic press:
    J. Chem. Phys. (rok: 2014, tom: 140, strony: 94105), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4866902 - link to the publication
  4. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase
    Authors:
    Trang Truc Nguyen, Man Hoang Viet, and Mai Suan Li
    Academic press:
    The Scientific World Journal (rok: 2014, tom: 2014, strony: Article number 536084), Wydawca: Hindawi
    Status:
    Published
    DOI:
    10.1155/2014/536084 - link to the publication
  5. Top-leads from natural products for treatment of Alzheimer's disease: Docking and molecular dynamics study
    Authors:
    Son Tung Ngo and Mai Suan Li
    Academic press:
    Molecular Simulation (rok: 2013, tom: 39, strony: 279-291), Wydawca: Taylor & Francis
    Status:
    Published
    DOI:
    10.1080/08927022.2012.718769 - link to the publication
  6. Streered molecular dynamics – a promising tool for drug design
    Authors:
    Mai Suan Li and Binh Khanh Mai
    Academic press:
    Current Bioinformatics (rok: 2012, tom: 7, strony: 342-351), Wydawca: Bentham Science Publisher LTD
    Status:
    Published
    DOI:
    10.2174/1574893611207040342 - link to the publication
  7. Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models
    Authors:
    Nguyen Truong Co, Chin-Kun Hu, and Mai Suan Li
    Academic press:
    J. Chem. Phys. (rok: 2013, tom: 138, strony: 185101), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4804299 - link to the publication
  8. Amyloid β-protein and Alzheimer's disease: when computer simulations complement experimental studies
    Authors:
    J. Nasica-Labouze, Phuong Nguyen, F. Sterpone, O. Bertomieu, N-V. Buchete, S. Cote, A. De Simone, A. Doig, P. Fallen, A. Garcia, A. Laio, Mai Suan Li, S. Melchionna, N. Mousseau, Y. Mu, A. Paravastu, S. Pasquali, D. Resenman, B. Strodel, B. Tarus, J. Viles, T. Zang, C. Wang, and P. Derreumaux
    Academic press:
    Chemical Reviews (rok: 2015, tom: 115, strony: 3518-3563), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/cr500638n - link to the publication
  9. In silico and in vitro characterization of anti-amyloidogenic activity of vitamin K3 analogues for Alzheimer's disease
    Authors:
    P.D.Q. Huy, Y-C. Yu, Son Tung Ngo, Tran Van Thao, C-P Chen, M. S. Li, and Y-C Chen
    Academic press:
    Biochimica et Biophysica Acta-General Subjects (rok: 2013, tom: 1380, strony: 2960-2969), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bbagen.2012.12.026 - link to the publication
  10. New method for determining size of critical nucleus of fibril formation of polypeptide chains
    Authors:
    Nguyen Truong Co and Mai Suan Li
    Academic press:
    J. Chem. Phys. (rok: 2012, tom: 137, strony: 95101), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4749257 - link to the publication
  11. Effect of Taiwan Mutation (D7H) on Structures of Amyloid Beta Peptides: Replica Exchange Molecular Dynamics Study
    Authors:
    Phan Minh Truong, Man Hoang Viet, Phuong H. Nguyen, C. K. Hu, and Mai Suan Li
    Academic press:
    J. Phys. Chem. B (rok: 2014, tom: 118, strony: 8972), Wydawca: ACS Publishing
    Status:
    Published
    DOI:
    10.1021/jp503652s - link to the publication
  12. Inhibition of insulin amyloid fibrillization by glyco-acridines: anin vitro andin silico study
    Authors:
    Quan Van Vuong, Zuzana Bednarikova, Andrea Antosova, Pham Dinh Quoc Huy, Katarina Siposova, Nguyen Anh Tuan, Mai Suan Li and Zuzana Gazova
    Academic press:
    Med Chem Commun (rok: 2015, tom: 6, strony: 810), Wydawca: The Royal Society of Chemistry Publishing
    Status:
    Published
    DOI:
    10.1039/C5MD00004A - link to the publication
  13. In silico and in vitro study of binding affinity oftripeptides to amyloid beta fibrils: Implications for Alzheimer's disease
    Authors:
    Man Hoang Viet, Katarina Siposova, Zuzana Bednarikova, Andrea Antosova, Truc Trang Nguyen, Zuzana Gazova, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2015, tom: 119, strony: 5145), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.5b00006 - link to the publication
  14. Effect of the English familial disease mutation (H6R) on the monomers and dimers of Abeta and Abeta42
    Authors:
    Man Hoang Viet, Phuong H. Nguyen, P. Derreumaux, and Mai Suan Li
    Academic press:
    ACS Chem Neurosci. (rok: 2014, tom: 5, strony: 646), Wydawca: ACS Publishing
    Status:
    Published
    DOI:
    10.1021/cn500007j - link to the publication
  15. Binding of fullerenes to amyloid beta fibrils: Size matters
    Authors:
    Pham Dinh Quoc Huy and Mai Suan Li
    Academic press:
    Phys. Chem. Chem. Phys (rok: 2014, tom: 16, strony: 20030), Wydawca: The Royal Society of Chemistry Publishing
    Status:
    Published
    DOI:
    10.1039/c4cp02348j - link to the publication
  16. Amyloid peptide Ab40 inhibits aggregation of Ab42: evidence from molecular dynamics simulations
    Authors:
    Man Hoang Viet and Mai Suan Li
    Academic press:
    J. Chem. Phys. (rok: 2012, tom: 136, strony: 245105), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4817773 - link to the publication
  17. New method for determining size of critical nucleus of fibril formation of polypeptide chains
    Authors:
    Nguyen Truong Co and Mai Suan Li
    Academic press:
    J. Chem. Phys. (rok: 2012, tom: 137, strony: 95101), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4749257 - link to the publication
  18. Amyloid β-protein and Alzheimer's disease: when computer simulations complement experimental studies
    Authors:
    J. Nasica-Labouze, Phuong Nguyen, F. Sterpone, O. Bertomieu, N-V. Buchete, S. Cote, A. De Simone, A. Doig, P. Fallen, A. Garcia, A. Laio, Mai Suan Li, S. Melchionna, N. Mousseau, Y. Mu, A. Paravastu, S. Pasquali, D. Resenman, B. Strodel, B. Tarus, J. Viles, T. Zang, C. Wang, and P. Derreumaux
    Academic press:
    Chemical Reviews (rok: 2015, tom: 115, strony: 3518-3563), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/cr500638n - link to the publication
  19. Binding of fullerenes to amyloid beta fibrils: Size matters
    Authors:
    Pham Dinh Quoc Huy and Mai Suan Li
    Academic press:
    Phys. Chem. Chem. Phys (rok: 2014, tom: 16, strony: 20030), Wydawca: The Royal Society of Chemistry Publishing
    Status:
    Published
    DOI:
    10.1039/c4cp02348j - link to the publication
  20. Curcumin Binds to Ab40 Peptides and Fibrils Stronger Than Ibuprofen and Naproxen
    Authors:
    Son Tung Ngo and Mai Suan Li
    Academic press:
    J. Phys. Chem. B (rok: 2012, tom: 116, strony: 10165-10175), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/jp302506a - link to the publication
  21. Estimation of the binding free energy of AC1NX476 to HIV-1 protease wild-type and mutations using free energy perturbation method
    Authors:
    Son Tung Ngo, Binh Khanh Mai, Dinh Minh Hiep, and Mai Suan Li
    Academic press:
    Chem Biol Drug Design (rok: 2015, tom: 86, strony: 546–558), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1111/cbdd.12518 - link to the publication
  22. Inhibition of insulin amyloid fibrillization by glyco-acridines: anin vitro andin silico study
    Authors:
    Quan Van Vuong, Zuzana Bednarikova, Andrea Antosova, Pham Dinh Quoc Huy, Katarina Siposova, Nguyen Anh Tuan, Mai Suan Li and Zuzana Gazova
    Academic press:
    Med Chem Commun (rok: 2015, tom: 6, strony: 810), Wydawca: The Royal Society of Chemistry Publishing
    Status:
    Published
    DOI:
    10.1039/C5MD00004A - link to the publication
  23. Oligomerization of peptides LVEALYL and RGFFYT and their binding affinity to insulin
    Authors:
    H. -L. Chiang, S. T. Ngo, C. -J. Chen, C.-K. Hu, and M. S. Li
    Academic press:
    Plos One (rok: 2013, tom: 8, strony: e65358), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0065358 - link to the publication
  24. Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models
    Authors:
    Nguyen Truong Co, Chin-Kun Hu, and Mai Suan Li
    Academic press:
    J. Chem. Phys. (rok: 2013, tom: 138, strony: 185101), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4804299 - link to the publication
  25. A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain
    Authors:
    M. Kouza, C-K. Hu, Mai Suan Li, and A. Kolinski
    Academic press:
    J. Chem. Phys. (rok: 2013, tom: 139, strony: 65103), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.4817773 - link to the publication
  26. Binding of glyco-acridine derivatives to lysozyme leads to inhibition of amyloid fibrillization, Biomacromolecules
    Authors:
    V.Q. Vuong, K. Siposova,T.T. Nguyen, A. Antosova, L. Balogova, L. Drajna,J. Imrich, M. S. Li, and Z. Gazova
    Academic press:
    Biomacromolecules (rok: 2013, tom: 14, strony: 1035-1043), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/bm301891q - link to the publication
  27. Discovery of Dihydrochalcone as potential lead for Alzheimer's disease: in silico and in vitro study
    Authors:
    M. H. Viet, C-Y. Chen, C-K. Hu, Y-R. Chen, and Mai Suan Li
    Academic press:
    Plose One (rok: 2013, tom: 8, strony: e79151), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0079151 - link to the publication
  28. Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Ab40 and Ab42
    Authors:
    M.H. Viet, P.H. Nguyen, S.T. Ngo, Mai Suan Li, and P. Derreumaux
    Academic press:
    ACS Chemical Neuroscience (rok: 2013, tom: 4, strony: 1446), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/cn400110d - link to the publication
  29. Oligomerization of peptides LVEALYL and RGFFYT and their binding affinity to insulin
    Authors:
    H. -L. Chiang, S. T. Ngo, C. -J. Chen, C.-K. Hu, and M. S. Li
    Academic press:
    Plos One (rok: 2013, tom: 8, strony: e65358), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0065358 - link to the publication
  30. Top-leads from natural products for treatment of Alzheimer's disease: Docking and molecular dynamics study
    Authors:
    Son Tung Ngo and Mai Suan Li
    Academic press:
    Molecular Simulation (rok: 2013, tom: 39, strony: 279-291), Wydawca: Taylor & Francis
    Status:
    Published
    DOI:
    10.1080/08927022.2012.718769 - link to the publication
  31. Estimation of the binding free energy of AC1NX476 to HIV-1 protease wild-type and mutations using free energy perturbation method
    Authors:
    Son Tung Ngo, Binh Khanh Mai, Dinh Minh Hiep, and Mai Suan Li
    Academic press:
    Chem Biol Drug Design (rok: 2015, tom: 86, strony: 546–558), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1111/cbdd.12518 - link to the publication
  32. Binding of glyco-acridine derivatives to lysozyme leads to inhibition of amyloid fibrillization, Biomacromolecules
    Authors:
    V.Q. Vuong, K. Siposova,T.T. Nguyen, A. Antosova, L. Balogova, L. Drajna,J. Imrich, M. S. Li, and Z. Gazova
    Academic press:
    Biomacromolecules (rok: 2013, tom: 14, strony: 1035-1043), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/bm301891q - link to the publication
  33. Effect of Taiwan Mutation (D7H) on Structures of Amyloid Beta Peptides: Replica Exchange Molecular Dynamics Study
    Authors:
    Phan Minh Truong, Man Hoang Viet, Phuong H. Nguyen, C. K. Hu, and Mai Suan Li
    Academic press:
    J. Phys. Chem. B (rok: 2014, tom: 118, strony: 8972), Wydawca: ACS Publishing
    Status:
    Published
    DOI:
    10.1021/jp503652s - link to the publication
  34. In silico and in vitro study of binding affinity oftripeptides to amyloid beta fibrils: Implications for Alzheimer's disease
    Authors:
    Man Hoang Viet, Katarina Siposova, Zuzana Bednarikova, Andrea Antosova, Truc Trang Nguyen, Zuzana Gazova, and Mai Suan Li
    Academic press:
    J Phys Chem B (rok: 2015, tom: 119, strony: 5145), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.5b00006 - link to the publication
  35. Stationary Josephson current in junctions involving d-wave superconductors with charge density waves: the temperature dependence and deviations from the law of corresponding states
    Authors:
    Alexander M. Gabovich, Mai Suan Li, Henryk Szymczak, and Alexander I. Voitenko
    Academic press:
    EUROPEAN PHYSICAL JOURNAL B (rok: 2014, tom: 87, strony: 115), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1140/epjb/e2014-41063-0 - link to the publication
  36. Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Ab40 and Ab42
    Authors:
    M.H. Viet, P.H. Nguyen, S.T. Ngo, Mai Suan Li, and P. Derreumaux
    Academic press:
    ACS Chemical Neuroscience (rok: 2013, tom: 4, strony: 1446), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/cn400110d - link to the publication
  37. Discovery of Dihydrochalcone as potential lead for Alzheimer's disease: in silico and in vitro study
    Authors:
    M. H. Viet, C-Y. Chen, C-K. Hu, Y-R. Chen, and Mai Suan Li
    Academic press:
    Plose One (rok: 2013, tom: 8, strony: e79151), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0079151 - link to the publication
  38. Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase
    Authors:
    Trang Truc Nguyen, Man Hoang Viet, and Mai Suan Li
    Academic press:
    The Scientific World Journal (rok: 2014, tom: 2014, strony: Article number 536084), Wydawca: Hindawi
    Status:
    Published
    DOI:
    10.1155/2014/536084 - link to the publication

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