COST Action Epigenetic Chemical Biology CM1406

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COST Action Epigenetic Chemical Biology CM1406

Authors

Publications

Rational design and evaluation of selective HDAC inhibitors

Ružić, Dušan; Đoković, Nemanja; Petković, Miloš; Agbaba, Danica; Gul, Sheraz; Lahtela-Kakkonen, Maija; Ganesan, A.; Nikolić, Katarina

(European Cooperation in Science and Technology (COST), 2019) 

TY  - CONF
AU  - Ružić, Dušan
AU  - Đoković, Nemanja
AU  - Petković, Miloš
AU  - Agbaba, Danica
AU  - Gul, Sheraz
AU  - Lahtela-Kakkonen, Maija
AU  - Ganesan, A.
AU  - Nikolić, Katarina
PY  - 2019
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4945
PB  - European Cooperation in Science and Technology (COST)
C3  - COST Action CM1406 EpiChemBio WG1 meeting, Salerno, 4-5 March 2019.
T1  - Rational design and evaluation of selective HDAC inhibitors
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4945
ER  - 
@conference{
author = "Ružić, Dušan and Đoković, Nemanja and Petković, Miloš and Agbaba, Danica and Gul, Sheraz and Lahtela-Kakkonen, Maija and Ganesan, A. and Nikolić, Katarina",
year = "2019",
publisher = "European Cooperation in Science and Technology (COST)",
journal = "COST Action CM1406 EpiChemBio WG1 meeting, Salerno, 4-5 March 2019.",
title = "Rational design and evaluation of selective HDAC inhibitors",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4945"
}
Ružić, D., Đoković, N., Petković, M., Agbaba, D., Gul, S., Lahtela-Kakkonen, M., Ganesan, A.,& Nikolić, K.. (2019). Rational design and evaluation of selective HDAC inhibitors. in COST Action CM1406 EpiChemBio WG1 meeting, Salerno, 4-5 March 2019.
European Cooperation in Science and Technology (COST)..
https://hdl.handle.net/21.15107/rcub_farfar_4945
Ružić D, Đoković N, Petković M, Agbaba D, Gul S, Lahtela-Kakkonen M, Ganesan A, Nikolić K. Rational design and evaluation of selective HDAC inhibitors. in COST Action CM1406 EpiChemBio WG1 meeting, Salerno, 4-5 March 2019.. 2019;.
https://hdl.handle.net/21.15107/rcub_farfar_4945 .
Ružić, Dušan, Đoković, Nemanja, Petković, Miloš, Agbaba, Danica, Gul, Sheraz, Lahtela-Kakkonen, Maija, Ganesan, A., Nikolić, Katarina, "Rational design and evaluation of selective HDAC inhibitors" in COST Action CM1406 EpiChemBio WG1 meeting, Salerno, 4-5 March 2019. (2019),
https://hdl.handle.net/21.15107/rcub_farfar_4945 .

Computer-aided design of histone deacetylase inhibitors

Ružić, Dušan; Đoković, Nemanja; Petković, Miloš; Agbaba, Danica; Lahtela-Kakkonen, Maija; Nikolić, Katarina; Ganesan, A.

(2018) 

TY  - CONF
AU  - Ružić, Dušan
AU  - Đoković, Nemanja
AU  - Petković, Miloš
AU  - Agbaba, Danica
AU  - Lahtela-Kakkonen, Maija
AU  - Nikolić, Katarina
AU  - Ganesan, A.
PY  - 2018
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4950
C3  - Epigenetic Chemical Biology – Action CM1406, Computational Methods in Drug Design. Training School 22 – 24 March 2018, Istanbul, Turkey
T1  - Computer-aided design of histone deacetylase inhibitors
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4950
ER  - 
@conference{
author = "Ružić, Dušan and Đoković, Nemanja and Petković, Miloš and Agbaba, Danica and Lahtela-Kakkonen, Maija and Nikolić, Katarina and Ganesan, A.",
year = "2018",
journal = "Epigenetic Chemical Biology – Action CM1406, Computational Methods in Drug Design. Training School 22 – 24 March 2018, Istanbul, Turkey",
title = "Computer-aided design of histone deacetylase inhibitors",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4950"
}
Ružić, D., Đoković, N., Petković, M., Agbaba, D., Lahtela-Kakkonen, M., Nikolić, K.,& Ganesan, A.. (2018). Computer-aided design of histone deacetylase inhibitors. in Epigenetic Chemical Biology – Action CM1406, Computational Methods in Drug Design. Training School 22 – 24 March 2018, Istanbul, Turkey.
https://hdl.handle.net/21.15107/rcub_farfar_4950
Ružić D, Đoković N, Petković M, Agbaba D, Lahtela-Kakkonen M, Nikolić K, Ganesan A. Computer-aided design of histone deacetylase inhibitors. in Epigenetic Chemical Biology – Action CM1406, Computational Methods in Drug Design. Training School 22 – 24 March 2018, Istanbul, Turkey. 2018;.
https://hdl.handle.net/21.15107/rcub_farfar_4950 .
Ružić, Dušan, Đoković, Nemanja, Petković, Miloš, Agbaba, Danica, Lahtela-Kakkonen, Maija, Nikolić, Katarina, Ganesan, A., "Computer-aided design of histone deacetylase inhibitors" in Epigenetic Chemical Biology – Action CM1406, Computational Methods in Drug Design. Training School 22 – 24 March 2018, Istanbul, Turkey (2018),
https://hdl.handle.net/21.15107/rcub_farfar_4950 .

Computer-aided drug design of selective histone deacetylase inhibitors

Nikolić, Katarina; Ružić, Dušan; Đoković, Nemanja; Petković, Miloš; Agbaba, Danica; Lahtela-Kakkonen, Maija; Ganesan, A.

(iMedPub LTD, 2018) 

TY  - CONF
AU  - Nikolić, Katarina
AU  - Ružić, Dušan
AU  - Đoković, Nemanja
AU  - Petković, Miloš
AU  - Agbaba, Danica
AU  - Lahtela-Kakkonen, Maija
AU  - Ganesan, A.
PY  - 2018
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4929
AB  - The concept of gene expression is continuously explained with epigenetic modification. Post-translational histone acetylation and DNA methylation are dominant epigenetic alterations of the genome. Histone deacetylases (HDAC) play essential role in this process and therefore are very intensively investigated drug targets. The alteration in the structure and function of HDAC isoforms are identified in the pathogenesis of inflammation, cancer, and neurodegeneration. Eleven human HDAC isoforms are sharing a highly conserved catalytic domain. Among them, HDAC6 and SIRT2 are important for a wide range of diseases, due to their unique physiological functions. In our research, we have applied pharmacophore modelling, virtual screening, molecular docking and molecular dynamic methodologies for design and identification of selective HDAC6 and SIRT2 inhibitors. Recently resolved the crystal structure of catalytic domain II of human HDAC6 discovered a wide binding site essential for the substrate recognition. We have successfully used these structural features of human HDAC6 catalytic domain II to rationally design selective HDAC6 inhibitors. Newly published X-ray structures of selective ligand-SIRT2 complexes have revealed high conformational flexibility of this enzyme, and gave us more details about mechanism of action of sirtuin 2 inhibitors. Based on these findings we have performed molecular dynamic study of SIRT2 and tried to explain the conformational changes during enzyme catalysis. Since small number of selective HDAC modulators have been reported so far, rational design of HDAC6 and SIRT2 inhibitors are essential for further progress in discovery of epigenetic drugs.
PB  - iMedPub LTD
C3  - Journal of organic & inorganic chemistry
T1  - Computer-aided drug design of selective histone deacetylase inhibitors
SP  - 28
EP  - 28
DO  - 10.21767/2472-1123-C2-005
ER  - 
@conference{
author = "Nikolić, Katarina and Ružić, Dušan and Đoković, Nemanja and Petković, Miloš and Agbaba, Danica and Lahtela-Kakkonen, Maija and Ganesan, A.",
year = "2018",
abstract = "The concept of gene expression is continuously explained with epigenetic modification. Post-translational histone acetylation and DNA methylation are dominant epigenetic alterations of the genome. Histone deacetylases (HDAC) play essential role in this process and therefore are very intensively investigated drug targets. The alteration in the structure and function of HDAC isoforms are identified in the pathogenesis of inflammation, cancer, and neurodegeneration. Eleven human HDAC isoforms are sharing a highly conserved catalytic domain. Among them, HDAC6 and SIRT2 are important for a wide range of diseases, due to their unique physiological functions. In our research, we have applied pharmacophore modelling, virtual screening, molecular docking and molecular dynamic methodologies for design and identification of selective HDAC6 and SIRT2 inhibitors. Recently resolved the crystal structure of catalytic domain II of human HDAC6 discovered a wide binding site essential for the substrate recognition. We have successfully used these structural features of human HDAC6 catalytic domain II to rationally design selective HDAC6 inhibitors. Newly published X-ray structures of selective ligand-SIRT2 complexes have revealed high conformational flexibility of this enzyme, and gave us more details about mechanism of action of sirtuin 2 inhibitors. Based on these findings we have performed molecular dynamic study of SIRT2 and tried to explain the conformational changes during enzyme catalysis. Since small number of selective HDAC modulators have been reported so far, rational design of HDAC6 and SIRT2 inhibitors are essential for further progress in discovery of epigenetic drugs.",
publisher = "iMedPub LTD",
journal = "Journal of organic & inorganic chemistry",
title = "Computer-aided drug design of selective histone deacetylase inhibitors",
pages = "28-28",
doi = "10.21767/2472-1123-C2-005"
}
Nikolić, K., Ružić, D., Đoković, N., Petković, M., Agbaba, D., Lahtela-Kakkonen, M.,& Ganesan, A.. (2018). Computer-aided drug design of selective histone deacetylase inhibitors. in Journal of organic & inorganic chemistry
iMedPub LTD., 28-28.
https://doi.org/10.21767/2472-1123-C2-005
Nikolić K, Ružić D, Đoković N, Petković M, Agbaba D, Lahtela-Kakkonen M, Ganesan A. Computer-aided drug design of selective histone deacetylase inhibitors. in Journal of organic & inorganic chemistry. 2018;:28-28.
doi:10.21767/2472-1123-C2-005 .
Nikolić, Katarina, Ružić, Dušan, Đoković, Nemanja, Petković, Miloš, Agbaba, Danica, Lahtela-Kakkonen, Maija, Ganesan, A., "Computer-aided drug design of selective histone deacetylase inhibitors" in Journal of organic & inorganic chemistry (2018):28-28,
https://doi.org/10.21767/2472-1123-C2-005 . .
2

Development of cross metathesis for the design of HDAC inhibitors

Bouchet, Samuel; Linot, Camille; Ružić, Dušan; Agbaba, Danica; Fouchaq, Benoit; Roche, Joëlle; Nikolić, Katarina; bl, Christophe; Zwick, Vincent; Nurisso, Alessandra; Simoes-Pires, Claudia; Lehotzky, Attila; Ovadi, Judit; Cuendet, Muriel; Bertrand, Philippe

(2018) 

TY  - CONF
AU  - Bouchet, Samuel
AU  - Linot, Camille
AU  - Ružić, Dušan
AU  - Agbaba, Danica
AU  - Fouchaq, Benoit
AU  - Roche, Joëlle
AU  - Nikolić, Katarina
AU  - bl, Christophe
AU  - Zwick, Vincent
AU  - Nurisso, Alessandra
AU  - Simoes-Pires, Claudia
AU  - Lehotzky, Attila
AU  - Ovadi, Judit
AU  - Cuendet, Muriel
AU  - Bertrand, Philippe
PY  - 2018
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4927
C3  - 4th International Epigenetic congress EpiNanties 2018, 16-17. October 2018, Nanties, France.
T1  - Development of cross metathesis  for the design of HDAC inhibitors
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4927
ER  - 
@conference{
author = "Bouchet, Samuel and Linot, Camille and Ružić, Dušan and Agbaba, Danica and Fouchaq, Benoit and Roche, Joëlle and Nikolić, Katarina and bl, Christophe and Zwick, Vincent and Nurisso, Alessandra and Simoes-Pires, Claudia and Lehotzky, Attila and Ovadi, Judit and Cuendet, Muriel and Bertrand, Philippe",
year = "2018",
journal = "4th International Epigenetic congress EpiNanties 2018, 16-17. October 2018, Nanties, France.",
title = "Development of cross metathesis  for the design of HDAC inhibitors",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4927"
}
Bouchet, S., Linot, C., Ružić, D., Agbaba, D., Fouchaq, B., Roche, J., Nikolić, K., bl, C., Zwick, V., Nurisso, A., Simoes-Pires, C., Lehotzky, A., Ovadi, J., Cuendet, M.,& Bertrand, P.. (2018). Development of cross metathesis  for the design of HDAC inhibitors. in 4th International Epigenetic congress EpiNanties 2018, 16-17. October 2018, Nanties, France..
https://hdl.handle.net/21.15107/rcub_farfar_4927
Bouchet S, Linot C, Ružić D, Agbaba D, Fouchaq B, Roche J, Nikolić K, bl C, Zwick V, Nurisso A, Simoes-Pires C, Lehotzky A, Ovadi J, Cuendet M, Bertrand P. Development of cross metathesis  for the design of HDAC inhibitors. in 4th International Epigenetic congress EpiNanties 2018, 16-17. October 2018, Nanties, France.. 2018;.
https://hdl.handle.net/21.15107/rcub_farfar_4927 .
Bouchet, Samuel, Linot, Camille, Ružić, Dušan, Agbaba, Danica, Fouchaq, Benoit, Roche, Joëlle, Nikolić, Katarina, bl, Christophe, Zwick, Vincent, Nurisso, Alessandra, Simoes-Pires, Claudia, Lehotzky, Attila, Ovadi, Judit, Cuendet, Muriel, Bertrand, Philippe, "Development of cross metathesis  for the design of HDAC inhibitors" in 4th International Epigenetic congress EpiNanties 2018, 16-17. October 2018, Nanties, France. (2018),
https://hdl.handle.net/21.15107/rcub_farfar_4927 .

HyDroxAmiC acid in HDAC inhibitors – Valuable, though not irreplaceable Zinc Binding Group

Ružić, Dušan; Petković, Miloš; Agbaba, Danica; Nikolić, Katarina; Ganesan, A.

(2017) 

TY  - CONF
AU  - Ružić, Dušan
AU  - Petković, Miloš
AU  - Agbaba, Danica
AU  - Nikolić, Katarina
AU  - Ganesan, A.
PY  - 2017
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4944
C3  - COST Action EpiChemBio CM1406, The Many Faces of Epigenetics. Multidisciplinary Perspectives "over" Genetics, 6-8 December 2017, Maison Française d'Oxford
T1  - HyDroxAmiC acid in HDAC inhibitors – Valuable, though not irreplaceable Zinc Binding Group
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4944
ER  - 
@conference{
author = "Ružić, Dušan and Petković, Miloš and Agbaba, Danica and Nikolić, Katarina and Ganesan, A.",
year = "2017",
journal = "COST Action EpiChemBio CM1406, The Many Faces of Epigenetics. Multidisciplinary Perspectives "over" Genetics, 6-8 December 2017, Maison Française d'Oxford",
title = "HyDroxAmiC acid in HDAC inhibitors – Valuable, though not irreplaceable Zinc Binding Group",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4944"
}
Ružić, D., Petković, M., Agbaba, D., Nikolić, K.,& Ganesan, A.. (2017). HyDroxAmiC acid in HDAC inhibitors – Valuable, though not irreplaceable Zinc Binding Group. in COST Action EpiChemBio CM1406, The Many Faces of Epigenetics. Multidisciplinary Perspectives "over" Genetics, 6-8 December 2017, Maison Française d'Oxford.
https://hdl.handle.net/21.15107/rcub_farfar_4944
Ružić D, Petković M, Agbaba D, Nikolić K, Ganesan A. HyDroxAmiC acid in HDAC inhibitors – Valuable, though not irreplaceable Zinc Binding Group. in COST Action EpiChemBio CM1406, The Many Faces of Epigenetics. Multidisciplinary Perspectives "over" Genetics, 6-8 December 2017, Maison Française d'Oxford. 2017;.
https://hdl.handle.net/21.15107/rcub_farfar_4944 .
Ružić, Dušan, Petković, Miloš, Agbaba, Danica, Nikolić, Katarina, Ganesan, A., "HyDroxAmiC acid in HDAC inhibitors – Valuable, though not irreplaceable Zinc Binding Group" in COST Action EpiChemBio CM1406, The Many Faces of Epigenetics. Multidisciplinary Perspectives "over" Genetics, 6-8 December 2017, Maison Française d'Oxford (2017),
https://hdl.handle.net/21.15107/rcub_farfar_4944 .

Molecular docking studies into new crystal second catalytic domain of HDAC6

Ružić, Dušan; Nikolić, Katarina; Agbaba, Danica; Ganesan, A.

(2017) 

TY  - CONF
AU  - Ružić, Dušan
AU  - Nikolić, Katarina
AU  - Agbaba, Danica
AU  - Ganesan, A.
PY  - 2017
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4941
C3  - CM1406 – Epigenetic Chemical Biology (EPICHEMBIO) – COST CM1406. WG1 Scientific Workshop – EPIGENETIC CHEMICAL PROBES. Belgrade, 16th January 2017
T1  - Molecular docking studies into new crystal second catalytic domain of HDAC6
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4941
ER  - 
@conference{
author = "Ružić, Dušan and Nikolić, Katarina and Agbaba, Danica and Ganesan, A.",
year = "2017",
journal = "CM1406 – Epigenetic Chemical Biology (EPICHEMBIO) – COST CM1406. WG1 Scientific Workshop – EPIGENETIC CHEMICAL PROBES. Belgrade, 16th January 2017",
title = "Molecular docking studies into new crystal second catalytic domain of HDAC6",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4941"
}
Ružić, D., Nikolić, K., Agbaba, D.,& Ganesan, A.. (2017). Molecular docking studies into new crystal second catalytic domain of HDAC6. in CM1406 – Epigenetic Chemical Biology (EPICHEMBIO) – COST CM1406. WG1 Scientific Workshop – EPIGENETIC CHEMICAL PROBES. Belgrade, 16th January 2017.
https://hdl.handle.net/21.15107/rcub_farfar_4941
Ružić D, Nikolić K, Agbaba D, Ganesan A. Molecular docking studies into new crystal second catalytic domain of HDAC6. in CM1406 – Epigenetic Chemical Biology (EPICHEMBIO) – COST CM1406. WG1 Scientific Workshop – EPIGENETIC CHEMICAL PROBES. Belgrade, 16th January 2017. 2017;.
https://hdl.handle.net/21.15107/rcub_farfar_4941 .
Ružić, Dušan, Nikolić, Katarina, Agbaba, Danica, Ganesan, A., "Molecular docking studies into new crystal second catalytic domain of HDAC6" in CM1406 – Epigenetic Chemical Biology (EPICHEMBIO) – COST CM1406. WG1 Scientific Workshop – EPIGENETIC CHEMICAL PROBES. Belgrade, 16th January 2017 (2017),
https://hdl.handle.net/21.15107/rcub_farfar_4941 .

Contemporary approaches in design of novel histone-deacetylase 6 inhibitor

Ružić, Dušan; Nikolić, Katarina; Agbaba, Danica

(2015) 

TY  - CONF
AU  - Ružić, Dušan
AU  - Nikolić, Katarina
AU  - Agbaba, Danica
PY  - 2015
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4949
C3  - COST conference CM1406 EpiChemBio, September 28-29, 2015, Budapest, Hungary
T1  - Contemporary approaches in design of novel histone-deacetylase 6 inhibitor
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4949
ER  - 
@conference{
author = "Ružić, Dušan and Nikolić, Katarina and Agbaba, Danica",
year = "2015",
journal = "COST conference CM1406 EpiChemBio, September 28-29, 2015, Budapest, Hungary",
title = "Contemporary approaches in design of novel histone-deacetylase 6 inhibitor",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4949"
}
Ružić, D., Nikolić, K.,& Agbaba, D.. (2015). Contemporary approaches in design of novel histone-deacetylase 6 inhibitor. in COST conference CM1406 EpiChemBio, September 28-29, 2015, Budapest, Hungary.
https://hdl.handle.net/21.15107/rcub_farfar_4949
Ružić D, Nikolić K, Agbaba D. Contemporary approaches in design of novel histone-deacetylase 6 inhibitor. in COST conference CM1406 EpiChemBio, September 28-29, 2015, Budapest, Hungary. 2015;.
https://hdl.handle.net/21.15107/rcub_farfar_4949 .
Ružić, Dušan, Nikolić, Katarina, Agbaba, Danica, "Contemporary approaches in design of novel histone-deacetylase 6 inhibitor" in COST conference CM1406 EpiChemBio, September 28-29, 2015, Budapest, Hungary (2015),
https://hdl.handle.net/21.15107/rcub_farfar_4949 .