TY  - CONF
AU  - Ružić, Dušan
AU  - Petković, Miloš
AU  - Đoković, Nemanja
AU  - Santibanez, Juan
AU  - Pavić, Aleksandar
AU  - Ganesan, A.
AU  - Srdić Rajić, Tatjana
AU  - Nikolić, Katarina
PY  - 2023
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/5074
AB  - Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer that has poor survival rates due to the absence of specific molecular markers such as estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). In the era of precision oncology, it is recognized that an imbalance in post-translational modifications of histones, such as histone lysine acetylation and deacetylation, is closely linked to tumor initiation and progression. Two groups of enzymes control the reversible nature of histone post-translational acetylation: histone acetyltransferases (HATs) and histone deacetylases (HDACs). Isoform-specific targeting of HDACs is considered a rational strategy to develop safe anticancer therapeutics compared to non-selective HDAC inhibitors. However, non-selective HDAC inhibitors have been more extensively studied in clinical trials. This work presents the design and discovery of potent HDAC inhibitors that selectively target HDAC6 isozyme, using 1-benzhydryl piperazine as a surface recognition group with different hydrocarbon linkers. Through in vitro screening, two HDAC6-selective inhibitors with nanomolar IC50 values and two non-selective HDAC inhibitors were identified. Structure-based molecular modelling was utilized to investigate the impact of linker chemistry on the potency of synthesized inhibitors against HDAC6. The anti-cancer, anti-migratory, and anti-invasive activities of these compounds were evaluated using breast cancer cell lines (MDA-MB-231 and MCF-7). Experiments on a zebrafish MDA-MB-231 xenograft model demonstrated that a novel non-selective HDAC inhibitor (8b) with a seven-carbon-atom linker exhibited potent effects against tumor growth, metastasis, and angiogenesis at low micromolar concentrations.
PB  - Serbian Association on for Cancer Research Belgrade, Serbia
C3  - Oncology
Insights
T1  - Discovery of novel HDAC inhibitors for therapy of triple-negative breast cancer – preclinical study
VL  - 1
UR  - https://hdl.handle.net/21.15107/rcub_farfar_5074
ER  - 

@conference{
author = "Ružić, Dušan and Petković, Miloš and Đoković, Nemanja and Santibanez, Juan and Pavić, Aleksandar and Ganesan, A. and Srdić Rajić, Tatjana and Nikolić, Katarina",
year = "2023",
abstract = "Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer that has poor survival rates due to the absence of specific molecular markers such as estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). In the era of precision oncology, it is recognized that an imbalance in post-translational modifications of histones, such as histone lysine acetylation and deacetylation, is closely linked to tumor initiation and progression. Two groups of enzymes control the reversible nature of histone post-translational acetylation: histone acetyltransferases (HATs) and histone deacetylases (HDACs). Isoform-specific targeting of HDACs is considered a rational strategy to develop safe anticancer therapeutics compared to non-selective HDAC inhibitors. However, non-selective HDAC inhibitors have been more extensively studied in clinical trials. This work presents the design and discovery of potent HDAC inhibitors that selectively target HDAC6 isozyme, using 1-benzhydryl piperazine as a surface recognition group with different hydrocarbon linkers. Through in vitro screening, two HDAC6-selective inhibitors with nanomolar IC50 values and two non-selective HDAC inhibitors were identified. Structure-based molecular modelling was utilized to investigate the impact of linker chemistry on the potency of synthesized inhibitors against HDAC6. The anti-cancer, anti-migratory, and anti-invasive activities of these compounds were evaluated using breast cancer cell lines (MDA-MB-231 and MCF-7). Experiments on a zebrafish MDA-MB-231 xenograft model demonstrated that a novel non-selective HDAC inhibitor (8b) with a seven-carbon-atom linker exhibited potent effects against tumor growth, metastasis, and angiogenesis at low micromolar concentrations.",
publisher = "Serbian Association on for Cancer Research Belgrade, Serbia",
journal = "Oncology
Insights",
title = "Discovery of novel HDAC inhibitors for therapy of triple-negative breast cancer – preclinical study",
volume = "1",
url = "https://hdl.handle.net/21.15107/rcub_farfar_5074"
}

Ružić, D., Petković, M., Đoković, N., Santibanez, J., Pavić, A., Ganesan, A., Srdić Rajić, T.,& Nikolić, K.. (2023). Discovery of novel HDAC inhibitors for therapy of triple-negative breast cancer – preclinical study. in Oncology
Insights
Serbian Association on for Cancer Research Belgrade, Serbia., 1.
https://hdl.handle.net/21.15107/rcub_farfar_5074

Ružić D, Petković M, Đoković N, Santibanez J, Pavić A, Ganesan A, Srdić Rajić T, Nikolić K. Discovery of novel HDAC inhibitors for therapy of triple-negative breast cancer – preclinical study. in Oncology
Insights. 2023;1.
https://hdl.handle.net/21.15107/rcub_farfar_5074 .

Ružić, Dušan, Petković, Miloš, Đoković, Nemanja, Santibanez, Juan, Pavić, Aleksandar, Ganesan, A., Srdić Rajić, Tatjana, Nikolić, Katarina, "Discovery of novel HDAC inhibitors for therapy of triple-negative breast cancer – preclinical study" in Oncology
Insights, 1 (2023),
https://hdl.handle.net/21.15107/rcub_farfar_5074 .

TY  - JOUR
AU  - Bulut, Ipek
AU  - Lee, Adam
AU  - Cevatemre, Buse
AU  - Ružić, Dušan
AU  - Belle, Roman
AU  - Kawamura, Akane
AU  - Gul, Sheraz
AU  - Nikolić, Katarina
AU  - Ganesan, A.
AU  - Acilan, Ceyda
PY  - 2022
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4340
AB  - Defects in epigenetic pathways are key drivers of oncogenic cell proliferation. We developed a LSD1/HDAC6 multitargeting inhibitor (iDual), a hydroxamic acid analogue of the clinical candidate LSD1 inhibitor GSK2879552. iDual inhibits both targets with IC50 values of 540, 110, and 290 nM, respectively, against LSD1, HDAC6, and HDAC8. We compared its activity to structurally similar control probes that act by HDAC or LSD1 inhibition alone, as well as an inactive null compound. iDual inhibited the growth of leukemia cell lines at a higher level than GSK2879552 with micromolar IC50 values. Dual engagement with LSD1 and HDAC6 was supported by dose dependent increases in substrate levels, biomarkers, and cellular thermal shift assay. Both histone methylation and acetylation of tubulin were increased, while acetylated histone levels were only mildly affected, indicating selectivity for HDAC6. Downstream gene expression (CD11b, CD86, p21) was also elevated in response to iDual treatment. Remarkably, iDual synergized with doxorubicin, triggering significant levels of apoptosis with a sublethal concentration of the drug. While mechanistic studies did not reveal changes in DNA repair or drug efflux pathways, the expression of AGPAT9, ALOX5, BTG1, HIPK2, IFI44L, and LRP1, previously implicated in doxorubicin sensitivity, was significantly elevated.
PB  - MDPI
T2  - Cancers
T1  - Dual LSD1 and HDAC6 Inhibition Induces Doxorubicin Sensitivity in Acute Myeloid Leukemia Cells
VL  - 14
IS  - 23
DO  - 10.3390/cancers14236014
ER  - 

@article{
author = "Bulut, Ipek and Lee, Adam and Cevatemre, Buse and Ružić, Dušan and Belle, Roman and Kawamura, Akane and Gul, Sheraz and Nikolić, Katarina and Ganesan, A. and Acilan, Ceyda",
year = "2022",
abstract = "Defects in epigenetic pathways are key drivers of oncogenic cell proliferation. We developed a LSD1/HDAC6 multitargeting inhibitor (iDual), a hydroxamic acid analogue of the clinical candidate LSD1 inhibitor GSK2879552. iDual inhibits both targets with IC50 values of 540, 110, and 290 nM, respectively, against LSD1, HDAC6, and HDAC8. We compared its activity to structurally similar control probes that act by HDAC or LSD1 inhibition alone, as well as an inactive null compound. iDual inhibited the growth of leukemia cell lines at a higher level than GSK2879552 with micromolar IC50 values. Dual engagement with LSD1 and HDAC6 was supported by dose dependent increases in substrate levels, biomarkers, and cellular thermal shift assay. Both histone methylation and acetylation of tubulin were increased, while acetylated histone levels were only mildly affected, indicating selectivity for HDAC6. Downstream gene expression (CD11b, CD86, p21) was also elevated in response to iDual treatment. Remarkably, iDual synergized with doxorubicin, triggering significant levels of apoptosis with a sublethal concentration of the drug. While mechanistic studies did not reveal changes in DNA repair or drug efflux pathways, the expression of AGPAT9, ALOX5, BTG1, HIPK2, IFI44L, and LRP1, previously implicated in doxorubicin sensitivity, was significantly elevated.",
publisher = "MDPI",
journal = "Cancers",
title = "Dual LSD1 and HDAC6 Inhibition Induces Doxorubicin Sensitivity in Acute Myeloid Leukemia Cells",
volume = "14",
number = "23",
doi = "10.3390/cancers14236014"
}

Bulut, I., Lee, A., Cevatemre, B., Ružić, D., Belle, R., Kawamura, A., Gul, S., Nikolić, K., Ganesan, A.,& Acilan, C.. (2022). Dual LSD1 and HDAC6 Inhibition Induces Doxorubicin Sensitivity in Acute Myeloid Leukemia Cells. in Cancers
MDPI., 14(23).
https://doi.org/10.3390/cancers14236014

Bulut I, Lee A, Cevatemre B, Ružić D, Belle R, Kawamura A, Gul S, Nikolić K, Ganesan A, Acilan C. Dual LSD1 and HDAC6 Inhibition Induces Doxorubicin Sensitivity in Acute Myeloid Leukemia Cells. in Cancers. 2022;14(23).
doi:10.3390/cancers14236014 .

Bulut, Ipek, Lee, Adam, Cevatemre, Buse, Ružić, Dušan, Belle, Roman, Kawamura, Akane, Gul, Sheraz, Nikolić, Katarina, Ganesan, A., Acilan, Ceyda, "Dual LSD1 and HDAC6 Inhibition Induces Doxorubicin Sensitivity in Acute Myeloid Leukemia Cells" in Cancers, 14, no. 23 (2022),
https://doi.org/10.3390/cancers14236014 . .

TY  - GEN
AU  - Ružić, Dušan
AU  - Ellinger, Bernhard
AU  - Đoković, Nemanja
AU  - Santibanez, Juan
AU  - Ganesan, A.
AU  - Pavić, Aleksandar
AU  - Srdić Rajić, Tatjana
AU  - Petković, Miloš
AU  - Nikolić, Katarina
PY  - 2022
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4951
PB  - Institute Pasteur, France
T2  - Journal Club on Drug Design, Institute Pasteur, Paris, France November 25 2022
T1  - Identification of novel 1-benzhydryl-piperazine derivatives as Histone Deacetylase inhibitors using Fragment-based drug design strategy
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4951
ER  - 

@misc{
author = "Ružić, Dušan and Ellinger, Bernhard and Đoković, Nemanja and Santibanez, Juan and Ganesan, A. and Pavić, Aleksandar and Srdić Rajić, Tatjana and Petković, Miloš and Nikolić, Katarina",
year = "2022",
publisher = "Institute Pasteur, France",
journal = "Journal Club on Drug Design, Institute Pasteur, Paris, France November 25 2022",
title = "Identification of novel 1-benzhydryl-piperazine derivatives as Histone Deacetylase inhibitors using Fragment-based drug design strategy",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4951"
}

Ružić, D., Ellinger, B., Đoković, N., Santibanez, J., Ganesan, A., Pavić, A., Srdić Rajić, T., Petković, M.,& Nikolić, K.. (2022). Identification of novel 1-benzhydryl-piperazine derivatives as Histone Deacetylase inhibitors using Fragment-based drug design strategy. in Journal Club on Drug Design, Institute Pasteur, Paris, France November 25 2022
Institute Pasteur, France..
https://hdl.handle.net/21.15107/rcub_farfar_4951

Ružić D, Ellinger B, Đoković N, Santibanez J, Ganesan A, Pavić A, Srdić Rajić T, Petković M, Nikolić K. Identification of novel 1-benzhydryl-piperazine derivatives as Histone Deacetylase inhibitors using Fragment-based drug design strategy. in Journal Club on Drug Design, Institute Pasteur, Paris, France November 25 2022. 2022;.
https://hdl.handle.net/21.15107/rcub_farfar_4951 .

Ružić, Dušan, Ellinger, Bernhard, Đoković, Nemanja, Santibanez, Juan, Ganesan, A., Pavić, Aleksandar, Srdić Rajić, Tatjana, Petković, Miloš, Nikolić, Katarina, "Identification of novel 1-benzhydryl-piperazine derivatives as Histone Deacetylase inhibitors using Fragment-based drug design strategy" in Journal Club on Drug Design, Institute Pasteur, Paris, France November 25 2022 (2022),
https://hdl.handle.net/21.15107/rcub_farfar_4951 .

TY  - CONF
AU  - Ružić, Dušan
AU  - Đoković, Nemanja
AU  - Petković, Miloš
AU  - Gul, Sheraz
AU  - Lahtela‐Kakkonen, Maija
AU  - Ganesan, A.
AU  - Nikolić, Katarina
PY  - 2022
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4739
PB  - American Chemical Society Division of Medicinal Chemistry
C3  - 37th ACS National Medicinal Chemistry Symposium - American Chemical Society Division of Medicinal Chemistry, Book of Abstracts
T1  - Computer-aided drug design and evaluation of selective inhibitors against cytoplasmic histone deacetylases
SP  - 125
EP  - 125
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4739
ER  - 

@conference{
author = "Ružić, Dušan and Đoković, Nemanja and Petković, Miloš and Gul, Sheraz and Lahtela‐Kakkonen, Maija and Ganesan, A. and Nikolić, Katarina",
year = "2022",
publisher = "American Chemical Society Division of Medicinal Chemistry",
journal = "37th ACS National Medicinal Chemistry Symposium - American Chemical Society Division of Medicinal Chemistry, Book of Abstracts",
title = "Computer-aided drug design and evaluation of selective inhibitors against cytoplasmic histone deacetylases",
pages = "125-125",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4739"
}

Ružić, D., Đoković, N., Petković, M., Gul, S., Lahtela‐Kakkonen, M., Ganesan, A.,& Nikolić, K.. (2022). Computer-aided drug design and evaluation of selective inhibitors against cytoplasmic histone deacetylases. in 37th ACS National Medicinal Chemistry Symposium - American Chemical Society Division of Medicinal Chemistry, Book of Abstracts
American Chemical Society Division of Medicinal Chemistry., 125-125.
https://hdl.handle.net/21.15107/rcub_farfar_4739

Ružić D, Đoković N, Petković M, Gul S, Lahtela‐Kakkonen M, Ganesan A, Nikolić K. Computer-aided drug design and evaluation of selective inhibitors against cytoplasmic histone deacetylases. in 37th ACS National Medicinal Chemistry Symposium - American Chemical Society Division of Medicinal Chemistry, Book of Abstracts. 2022;:125-125.
https://hdl.handle.net/21.15107/rcub_farfar_4739 .

Ružić, Dušan, Đoković, Nemanja, Petković, Miloš, Gul, Sheraz, Lahtela‐Kakkonen, Maija, Ganesan, A., Nikolić, Katarina, "Computer-aided drug design and evaluation of selective inhibitors against cytoplasmic histone deacetylases" in 37th ACS National Medicinal Chemistry Symposium - American Chemical Society Division of Medicinal Chemistry, Book of Abstracts (2022):125-125,
https://hdl.handle.net/21.15107/rcub_farfar_4739 .

TY  - CONF
AU  - Ružić, Dušan
AU  - Đoković, Nemanja
AU  - Petković, Miloš
AU  - Gul, Sheraz
AU  - Lahtela‐Kakkonen, Maija
AU  - Ganesan, A.
AU  - Srdić-Rajić, Tatjana
AU  - Nikolić, Katarina
PY  - 2022
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4763
PB  - European Federation for Medicinal Chemistry and Chemical Biology (EFMC)
PB  - Société de Chimie Thérapeutique (SCT)
C3  - EFMC-ISMC, XXVII EFMC International Symposium on Medicinal Chemistry, Book of Abstracts
T1  - Rational design and in vitro evaluation of selective inhibitors of cytoplasmic histone deacetylases SIRT2 and HDAC6
SP  - 141
EP  - 141
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4763
ER  - 

@conference{
author = "Ružić, Dušan and Đoković, Nemanja and Petković, Miloš and Gul, Sheraz and Lahtela‐Kakkonen, Maija and Ganesan, A. and Srdić-Rajić, Tatjana and Nikolić, Katarina",
year = "2022",
publisher = "European Federation for Medicinal Chemistry and Chemical Biology (EFMC), Société de Chimie Thérapeutique (SCT)",
journal = "EFMC-ISMC, XXVII EFMC International Symposium on Medicinal Chemistry, Book of Abstracts",
title = "Rational design and in vitro evaluation of selective inhibitors of cytoplasmic histone deacetylases SIRT2 and HDAC6",
pages = "141-141",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4763"
}

Ružić, D., Đoković, N., Petković, M., Gul, S., Lahtela‐Kakkonen, M., Ganesan, A., Srdić-Rajić, T.,& Nikolić, K.. (2022). Rational design and in vitro evaluation of selective inhibitors of cytoplasmic histone deacetylases SIRT2 and HDAC6. in EFMC-ISMC, XXVII EFMC International Symposium on Medicinal Chemistry, Book of Abstracts
European Federation for Medicinal Chemistry and Chemical Biology (EFMC)., 141-141.
https://hdl.handle.net/21.15107/rcub_farfar_4763

Ružić D, Đoković N, Petković M, Gul S, Lahtela‐Kakkonen M, Ganesan A, Srdić-Rajić T, Nikolić K. Rational design and in vitro evaluation of selective inhibitors of cytoplasmic histone deacetylases SIRT2 and HDAC6. in EFMC-ISMC, XXVII EFMC International Symposium on Medicinal Chemistry, Book of Abstracts. 2022;:141-141.
https://hdl.handle.net/21.15107/rcub_farfar_4763 .

Ružić, Dušan, Đoković, Nemanja, Petković, Miloš, Gul, Sheraz, Lahtela‐Kakkonen, Maija, Ganesan, A., Srdić-Rajić, Tatjana, Nikolić, Katarina, "Rational design and in vitro evaluation of selective inhibitors of cytoplasmic histone deacetylases SIRT2 and HDAC6" in EFMC-ISMC, XXVII EFMC International Symposium on Medicinal Chemistry, Book of Abstracts (2022):141-141,
https://hdl.handle.net/21.15107/rcub_farfar_4763 .

TY  - CONF
AU  - Ružić, Dušan
AU  - Đoković, Nemanja
AU  - Corentin, Bon
AU  - Petković, Miloš
AU  - Ellinger, Bertrand
AU  - Gul, Sheraz
AU  - Santibanez, Juan
AU  - Lahtela-Kakkonen, Maija
AU  - Halby, Ludovic
AU  - Ganesan, A.
AU  - Srdić Rajić, Tatjana
AU  - Arimondo, Paola
AU  - Nikolić, Katarina
PY  - 2021
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4938
C3  - e-EuCo-CTC 2021, Online conference, EuChemS Division of Computational and Theoretical Chemistry, November 18-19 2021
T1  - Epigenetic drug discovery: Successful examples of Computer-Aided Drug Designing of Histone Deacetylase (HDAC6 and SIRT2) and Histone Methyltransferase (DOT1L) inhibitors
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4938
ER  - 

@conference{
author = "Ružić, Dušan and Đoković, Nemanja and Corentin, Bon and Petković, Miloš and Ellinger, Bertrand and Gul, Sheraz and Santibanez, Juan and Lahtela-Kakkonen, Maija and Halby, Ludovic and Ganesan, A. and Srdić Rajić, Tatjana and Arimondo, Paola and Nikolić, Katarina",
year = "2021",
journal = "e-EuCo-CTC 2021, Online conference, EuChemS Division of Computational and Theoretical Chemistry, November 18-19 2021",
title = "Epigenetic drug discovery: Successful examples of Computer-Aided Drug Designing of Histone Deacetylase (HDAC6 and SIRT2) and Histone Methyltransferase (DOT1L) inhibitors",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4938"
}

Ružić, D., Đoković, N., Corentin, B., Petković, M., Ellinger, B., Gul, S., Santibanez, J., Lahtela-Kakkonen, M., Halby, L., Ganesan, A., Srdić Rajić, T., Arimondo, P.,& Nikolić, K.. (2021). Epigenetic drug discovery: Successful examples of Computer-Aided Drug Designing of Histone Deacetylase (HDAC6 and SIRT2) and Histone Methyltransferase (DOT1L) inhibitors. in e-EuCo-CTC 2021, Online conference, EuChemS Division of Computational and Theoretical Chemistry, November 18-19 2021.
https://hdl.handle.net/21.15107/rcub_farfar_4938

Ružić D, Đoković N, Corentin B, Petković M, Ellinger B, Gul S, Santibanez J, Lahtela-Kakkonen M, Halby L, Ganesan A, Srdić Rajić T, Arimondo P, Nikolić K. Epigenetic drug discovery: Successful examples of Computer-Aided Drug Designing of Histone Deacetylase (HDAC6 and SIRT2) and Histone Methyltransferase (DOT1L) inhibitors. in e-EuCo-CTC 2021, Online conference, EuChemS Division of Computational and Theoretical Chemistry, November 18-19 2021. 2021;.
https://hdl.handle.net/21.15107/rcub_farfar_4938 .

Ružić, Dušan, Đoković, Nemanja, Corentin, Bon, Petković, Miloš, Ellinger, Bertrand, Gul, Sheraz, Santibanez, Juan, Lahtela-Kakkonen, Maija, Halby, Ludovic, Ganesan, A., Srdić Rajić, Tatjana, Arimondo, Paola, Nikolić, Katarina, "Epigenetic drug discovery: Successful examples of Computer-Aided Drug Designing of Histone Deacetylase (HDAC6 and SIRT2) and Histone Methyltransferase (DOT1L) inhibitors" in e-EuCo-CTC 2021, Online conference, EuChemS Division of Computational and Theoretical Chemistry, November 18-19 2021 (2021),
https://hdl.handle.net/21.15107/rcub_farfar_4938 .

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  - Santibanez, Juan
AU  - Srdić-Rajić, Tatjana
AU  - Nikolić, Katarina
PY  - 2021
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4889
AB  - Histone deacetylases (HDACs) are epigenetic enzymes involved in regulation of histone posttranslational
modifications and gene expression. Since changed function of HDACs is involved in pathogenesis of cancer 1-3,
the HDAC inhibitors are extensive examined as promising anticancer agents. In our in silico study we have
combined structure-based, ligand-based, and fragment-based methodologies to design selective inhibitors against
cytoplasmic isoforms of HDAC, such as histone deacetylase 6 inhibitors (HDAC6) and SIRT2. The drug design
study has defined several promising selective HDAC6 and SIRT2 inhibitors for further synthesis and in vitro
testing. Based on the in vitro activities of the novel compounds in a panel of biochemical HDAC assays as well
as various cell-based assays were selected the most promising candidates for further investigation.
PB  - EFMC-ISMC
C3  - EFMC-ISMC, XXVI EFMC International Symposium on Medicinal Chemistry, Book of Abstracts
T1  - Rational design, synthesis and in vitro testing of selective HDAC6 and SIRT2 inhibitors
SP  - 360
EP  - 360
EP  - 
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4889
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 Santibanez, Juan and Srdić-Rajić, Tatjana and Nikolić, Katarina",
year = "2021",
abstract = "Histone deacetylases (HDACs) are epigenetic enzymes involved in regulation of histone posttranslational
modifications and gene expression. Since changed function of HDACs is involved in pathogenesis of cancer 1-3,
the HDAC inhibitors are extensive examined as promising anticancer agents. In our in silico study we have
combined structure-based, ligand-based, and fragment-based methodologies to design selective inhibitors against
cytoplasmic isoforms of HDAC, such as histone deacetylase 6 inhibitors (HDAC6) and SIRT2. The drug design
study has defined several promising selective HDAC6 and SIRT2 inhibitors for further synthesis and in vitro
testing. Based on the in vitro activities of the novel compounds in a panel of biochemical HDAC assays as well
as various cell-based assays were selected the most promising candidates for further investigation.",
publisher = "EFMC-ISMC",
journal = "EFMC-ISMC, XXVI EFMC International Symposium on Medicinal Chemistry, Book of Abstracts",
title = "Rational design, synthesis and in vitro testing of selective HDAC6 and SIRT2 inhibitors",
pages = "360-360-",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4889"
}

Ružić, D., Đoković, N., Petković, M., Agbaba, D., Gul, S., Lahtela‐Kakkonen, M., Ganesan, A., Santibanez, J., Srdić-Rajić, T.,& Nikolić, K.. (2021). Rational design, synthesis and in vitro testing of selective HDAC6 and SIRT2 inhibitors. in EFMC-ISMC, XXVI EFMC International Symposium on Medicinal Chemistry, Book of Abstracts
EFMC-ISMC., 360-360.
https://hdl.handle.net/21.15107/rcub_farfar_4889

Ružić D, Đoković N, Petković M, Agbaba D, Gul S, Lahtela‐Kakkonen M, Ganesan A, Santibanez J, Srdić-Rajić T, Nikolić K. Rational design, synthesis and in vitro testing of selective HDAC6 and SIRT2 inhibitors. in EFMC-ISMC, XXVI EFMC International Symposium on Medicinal Chemistry, Book of Abstracts. 2021;:360-360.
https://hdl.handle.net/21.15107/rcub_farfar_4889 .

Ružić, Dušan, Đoković, Nemanja, Petković, Miloš, Agbaba, Danica, Gul, Sheraz, Lahtela‐Kakkonen, Maija, Ganesan, A., Santibanez, Juan, Srdić-Rajić, Tatjana, Nikolić, Katarina, "Rational design, synthesis and in vitro testing of selective HDAC6 and SIRT2 inhibitors" in EFMC-ISMC, XXVI EFMC International Symposium on Medicinal Chemistry, Book of Abstracts (2021):360-360,
https://hdl.handle.net/21.15107/rcub_farfar_4889 .

TY  - CONF
AU  - Lee, Adam
AU  - Ganesan, A.
AU  - Bulut, İpek
AU  - Açılan Ayhan, Ceyda
AU  - Ružić, Dušan
AU  - Nikolić, Katarina
AU  - Gul, Sheraz
PY  - 2020
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4872
AB  - Epigenetic therapy is now a clinical reality with eight approved drugs that target
DNA methyltransferases, histone deacetylases (HDACs) and lysine
methyltransferases. A further recent development is the concept of epigenetic
multitargeting through the rational design of novel agents that combine the
inhibition of an epigenetic pathway with a second non-epigenetic target and five
such compounds have advanced to clinical development.
We are investigating the even newer concept of „epi-epi‟ drugs that inhibit two
separate epigenetic pathways. Such dual targeting agents have the potential to
achieve higher efficacy against proliferating cancer cells while reducing tunor
resistance. In this presentation, we report a selective dual histone deacetylase and
demethylase inhibitor with an IC50
LSD1 respectively. The compound was biologically profiled together with control
compounds that were either single inhibitors or inactive against either enzyme. The
dua inhibitor was active against a panel of leukemia cell lines at a micromolar level
and induced apoptosis. Target engagement asays such as CETSA were employed
to confirm the inhibition of HDAC6 and LSD1 in cells. Further experiments were
carried out to identify synergistic effects with clinically approved agents and
promising results were observed with doxorubicin.
PB  - COST Action 17104 (STRATAGEM)
C3  - COST Action 17104 (STRATAGEM) WG2 Meeting and International Online Symposium on “Synthesis and nanodelivery strategies for new therapeutic tools against Multidrug Resistant Tumours”, 15th December 2020, Abstract Boook
T1  - Multitargeting epi-epi drugs for multidrug reistance
SP  - 12
EP  - 12
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4872
ER  - 

@conference{
author = "Lee, Adam and Ganesan, A. and Bulut, İpek and Açılan Ayhan, Ceyda and Ružić, Dušan and Nikolić, Katarina and Gul, Sheraz",
year = "2020",
abstract = "Epigenetic therapy is now a clinical reality with eight approved drugs that target
DNA methyltransferases, histone deacetylases (HDACs) and lysine
methyltransferases. A further recent development is the concept of epigenetic
multitargeting through the rational design of novel agents that combine the
inhibition of an epigenetic pathway with a second non-epigenetic target and five
such compounds have advanced to clinical development.
We are investigating the even newer concept of „epi-epi‟ drugs that inhibit two
separate epigenetic pathways. Such dual targeting agents have the potential to
achieve higher efficacy against proliferating cancer cells while reducing tunor
resistance. In this presentation, we report a selective dual histone deacetylase and
demethylase inhibitor with an IC50
LSD1 respectively. The compound was biologically profiled together with control
compounds that were either single inhibitors or inactive against either enzyme. The
dua inhibitor was active against a panel of leukemia cell lines at a micromolar level
and induced apoptosis. Target engagement asays such as CETSA were employed
to confirm the inhibition of HDAC6 and LSD1 in cells. Further experiments were
carried out to identify synergistic effects with clinically approved agents and
promising results were observed with doxorubicin.",
publisher = "COST Action 17104 (STRATAGEM)",
journal = "COST Action 17104 (STRATAGEM) WG2 Meeting and International Online Symposium on “Synthesis and nanodelivery strategies for new therapeutic tools against Multidrug Resistant Tumours”, 15th December 2020, Abstract Boook",
title = "Multitargeting epi-epi drugs for multidrug reistance",
pages = "12-12",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4872"
}

Lee, A., Ganesan, A., Bulut, İ., Açılan Ayhan, C., Ružić, D., Nikolić, K.,& Gul, S.. (2020). Multitargeting epi-epi drugs for multidrug reistance. in COST Action 17104 (STRATAGEM) WG2 Meeting and International Online Symposium on “Synthesis and nanodelivery strategies for new therapeutic tools against Multidrug Resistant Tumours”, 15th December 2020, Abstract Boook
COST Action 17104 (STRATAGEM)., 12-12.
https://hdl.handle.net/21.15107/rcub_farfar_4872

Lee A, Ganesan A, Bulut İ, Açılan Ayhan C, Ružić D, Nikolić K, Gul S. Multitargeting epi-epi drugs for multidrug reistance. in COST Action 17104 (STRATAGEM) WG2 Meeting and International Online Symposium on “Synthesis and nanodelivery strategies for new therapeutic tools against Multidrug Resistant Tumours”, 15th December 2020, Abstract Boook. 2020;:12-12.
https://hdl.handle.net/21.15107/rcub_farfar_4872 .

Lee, Adam, Ganesan, A., Bulut, İpek, Açılan Ayhan, Ceyda, Ružić, Dušan, Nikolić, Katarina, Gul, Sheraz, "Multitargeting epi-epi drugs for multidrug reistance" in COST Action 17104 (STRATAGEM) WG2 Meeting and International Online Symposium on “Synthesis and nanodelivery strategies for new therapeutic tools against Multidrug Resistant Tumours”, 15th December 2020, Abstract Boook (2020):12-12,
https://hdl.handle.net/21.15107/rcub_farfar_4872 .

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/123456789/4946
PB  - EuChemS (European Chemical Society)
C3  - 12th European Conference on computational theoretical chemistry  (EUCO-CTC 2019), 1-5 September 2019, Perugia, Italy, Book of Abstracts
T1  - Computer-Aided Drug Design and Evaluation of Selective HDAC Inhibitors
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4946
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 = "EuChemS (European Chemical Society)",
journal = "12th European Conference on computational theoretical chemistry  (EUCO-CTC 2019), 1-5 September 2019, Perugia, Italy, Book of Abstracts",
title = "Computer-Aided Drug Design and Evaluation of Selective HDAC Inhibitors",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4946"
}

Ružić, D., Đoković, N., Petković, M., Agbaba, D., Gul, S., Lahtela-Kakkonen, M., Ganesan, A.,& Nikolić, K.. (2019). Computer-Aided Drug Design and Evaluation of Selective HDAC Inhibitors. in 12th European Conference on computational theoretical chemistry  (EUCO-CTC 2019), 1-5 September 2019, Perugia, Italy, Book of Abstracts
EuChemS (European Chemical Society)..
https://hdl.handle.net/21.15107/rcub_farfar_4946

Ružić D, Đoković N, Petković M, Agbaba D, Gul S, Lahtela-Kakkonen M, Ganesan A, Nikolić K. Computer-Aided Drug Design and Evaluation of Selective HDAC Inhibitors. in 12th European Conference on computational theoretical chemistry  (EUCO-CTC 2019), 1-5 September 2019, Perugia, Italy, Book of Abstracts. 2019;.
https://hdl.handle.net/21.15107/rcub_farfar_4946 .

Ružić, Dušan, Đoković, Nemanja, Petković, Miloš, Agbaba, Danica, Gul, Sheraz, Lahtela-Kakkonen, Maija, Ganesan, A., Nikolić, Katarina, "Computer-Aided Drug Design and Evaluation of Selective HDAC Inhibitors" in 12th European Conference on computational theoretical chemistry  (EUCO-CTC 2019), 1-5 September 2019, Perugia, Italy, Book of Abstracts (2019),
https://hdl.handle.net/21.15107/rcub_farfar_4946 .

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 .

TY  - JOUR
AU  - Ružić, Dušan
AU  - Petković, Miloš
AU  - Agbaba, Danica
AU  - Ganesan, A.
AU  - Nikolić, Katarina
PY  - 2019
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/3369
AB  - Histone deacetylase 6 (HDAC6) is unique hydrolase within HDAC family, having pleiotropic deacetylase activity against alpha-tubulin, cortactin and dynein. Comprehensively, HDAC6 controls cell motility, apoptosis and protein folding, whereas alterations in its structure and function are related to the pathogenesis of cancer, neurodegeneration and inflammation. To define structural motifs which guide HDAC6 selectivity, we developed and compared three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) models for HDAC1 and HDAC6 inhibitors. The reduction of the bias in conformer generation was supported by virtual docking study by using crystal structures of human HDAC1 and HDAC6 isoforms. Following these findings, the combined ligand-based and fragment-based drug design methodologies were used in the design of selective HDAC6 inhibitors. Group of the most promising novel ligands was selected based on the predicted HDAC6 selectivity, pharmacokinetic profile, synthetic tractability, and in silico cytotoxicity against the wide range of human cancer cell lines.
PB  - Wiley-VCH Verlag GMBH, Weinheim
T2  - Molecular Informatics
T1  - Combined Ligand and Fragment-based Drug Design of Selective Histone Deacetylase-6 Inhibitors
VL  - 38
IS  - 5
DO  - 10.1002/minf.201800083
ER  - 

@article{
author = "Ružić, Dušan and Petković, Miloš and Agbaba, Danica and Ganesan, A. and Nikolić, Katarina",
year = "2019",
abstract = "Histone deacetylase 6 (HDAC6) is unique hydrolase within HDAC family, having pleiotropic deacetylase activity against alpha-tubulin, cortactin and dynein. Comprehensively, HDAC6 controls cell motility, apoptosis and protein folding, whereas alterations in its structure and function are related to the pathogenesis of cancer, neurodegeneration and inflammation. To define structural motifs which guide HDAC6 selectivity, we developed and compared three-dimensional Quantitative Structure-Activity Relationship (3D-QSAR) models for HDAC1 and HDAC6 inhibitors. The reduction of the bias in conformer generation was supported by virtual docking study by using crystal structures of human HDAC1 and HDAC6 isoforms. Following these findings, the combined ligand-based and fragment-based drug design methodologies were used in the design of selective HDAC6 inhibitors. Group of the most promising novel ligands was selected based on the predicted HDAC6 selectivity, pharmacokinetic profile, synthetic tractability, and in silico cytotoxicity against the wide range of human cancer cell lines.",
publisher = "Wiley-VCH Verlag GMBH, Weinheim",
journal = "Molecular Informatics",
title = "Combined Ligand and Fragment-based Drug Design of Selective Histone Deacetylase-6 Inhibitors",
volume = "38",
number = "5",
doi = "10.1002/minf.201800083"
}

Ružić, D., Petković, M., Agbaba, D., Ganesan, A.,& Nikolić, K.. (2019). Combined Ligand and Fragment-based Drug Design of Selective Histone Deacetylase-6 Inhibitors. in Molecular Informatics
Wiley-VCH Verlag GMBH, Weinheim., 38(5).
https://doi.org/10.1002/minf.201800083

Ružić D, Petković M, Agbaba D, Ganesan A, Nikolić K. Combined Ligand and Fragment-based Drug Design of Selective Histone Deacetylase-6 Inhibitors. in Molecular Informatics. 2019;38(5).
doi:10.1002/minf.201800083 .

Ružić, Dušan, Petković, Miloš, Agbaba, Danica, Ganesan, A., Nikolić, Katarina, "Combined Ligand and Fragment-based Drug Design of Selective Histone Deacetylase-6 Inhibitors" in Molecular Informatics, 38, no. 5 (2019),
https://doi.org/10.1002/minf.201800083 . .

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 .

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 . .

TY  - CONF
AU  - Ružić, Dušan
AU  - Nikolić, Katarina
AU  - Petković, Miloš
AU  - Ganesan, A.
AU  - Agbaba, Danica
PY  - 2018
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4894
AB  - Activity of the histone deacetylases (HDACs) has an essential influence on histone posttranslational
modifications. Therefore, alterations in the structure and expression of HDACs isoforms are strongly related to
the pathogenesis of inflammation, cancer, and neurodegeneration. The HDACs became extensively examined
targets in novel drug discovery. The HDAC6 isoform is a non-histone cytoplasmic deacetylase, manly involved
in deacetylation of α-tubulin, cortactin, and heat shock protein 90 (Hsp90) [1]. Our rational drug design study
was focused on identification of selective histone deacetylase 6 (HDAC6) inhibitors by use of combined ligand
and structure based methodologies. Based on the 3D-QSAR (Quantitative Structure Activity Relationship)
modeling of HDAC6 inhibitors were defined specific molecular determinants for selective HDAC6 inhibition
and further applied for fragment based design of selective HDAC6 inhibitors. Recently resolved crystal structure
of second human catalytic domain of HDAC-6 enzyme (5EDU) [2] was used in virtual docking study of the
examined inhibitors.
PB  - Section for Medicinal Chemistry of the Slovenian Pharmaceutical Society
C3  - EFMC-ISMC, XXV EFMC International Symposium on Medicinal Chemistry, Book of Abstract
T1  - Rational drug design of histone deacetylase 6 inhibitors
SP  - 305
EP  - 305
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4894
ER  - 

@conference{
author = "Ružić, Dušan and Nikolić, Katarina and Petković, Miloš and Ganesan, A. and Agbaba, Danica",
year = "2018",
abstract = "Activity of the histone deacetylases (HDACs) has an essential influence on histone posttranslational
modifications. Therefore, alterations in the structure and expression of HDACs isoforms are strongly related to
the pathogenesis of inflammation, cancer, and neurodegeneration. The HDACs became extensively examined
targets in novel drug discovery. The HDAC6 isoform is a non-histone cytoplasmic deacetylase, manly involved
in deacetylation of α-tubulin, cortactin, and heat shock protein 90 (Hsp90) [1]. Our rational drug design study
was focused on identification of selective histone deacetylase 6 (HDAC6) inhibitors by use of combined ligand
and structure based methodologies. Based on the 3D-QSAR (Quantitative Structure Activity Relationship)
modeling of HDAC6 inhibitors were defined specific molecular determinants for selective HDAC6 inhibition
and further applied for fragment based design of selective HDAC6 inhibitors. Recently resolved crystal structure
of second human catalytic domain of HDAC-6 enzyme (5EDU) [2] was used in virtual docking study of the
examined inhibitors.",
publisher = "Section for Medicinal Chemistry of the Slovenian Pharmaceutical Society",
journal = "EFMC-ISMC, XXV EFMC International Symposium on Medicinal Chemistry, Book of Abstract",
title = "Rational drug design of histone deacetylase 6 inhibitors",
pages = "305-305",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4894"
}

Ružić, D., Nikolić, K., Petković, M., Ganesan, A.,& Agbaba, D.. (2018). Rational drug design of histone deacetylase 6 inhibitors. in EFMC-ISMC, XXV EFMC International Symposium on Medicinal Chemistry, Book of Abstract
Section for Medicinal Chemistry of the Slovenian Pharmaceutical Society., 305-305.
https://hdl.handle.net/21.15107/rcub_farfar_4894

Ružić D, Nikolić K, Petković M, Ganesan A, Agbaba D. Rational drug design of histone deacetylase 6 inhibitors. in EFMC-ISMC, XXV EFMC International Symposium on Medicinal Chemistry, Book of Abstract. 2018;:305-305.
https://hdl.handle.net/21.15107/rcub_farfar_4894 .

Ružić, Dušan, Nikolić, Katarina, Petković, Miloš, Ganesan, A., Agbaba, Danica, "Rational drug design of histone deacetylase 6 inhibitors" in EFMC-ISMC, XXV EFMC International Symposium on Medicinal Chemistry, Book of Abstract (2018):305-305,
https://hdl.handle.net/21.15107/rcub_farfar_4894 .

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 .

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 .

TY  - CONF
AU  - Ružić, Dušan
AU  - Nikolić, Katarina
AU  - Senćanski, Milan
AU  - Agbaba, Danica
AU  - Ganesan, A.
PY  - 2016
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4943
C3  - COST Action CM1406 EpichemBio (Epigenetic Chemical Biology), 15-16 September 2016, Groningen, Netherlands
T1  - Structural insight in HDAC-6 inhibition: Molecular docking studies of naphthalimide based HDAC inhibitors
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4943
ER  - 

@conference{
author = "Ružić, Dušan and Nikolić, Katarina and Senćanski, Milan and Agbaba, Danica and Ganesan, A.",
year = "2016",
journal = "COST Action CM1406 EpichemBio (Epigenetic Chemical Biology), 15-16 September 2016, Groningen, Netherlands",
title = "Structural insight in HDAC-6 inhibition: Molecular docking studies of naphthalimide based HDAC inhibitors",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4943"
}

Ružić, D., Nikolić, K., Senćanski, M., Agbaba, D.,& Ganesan, A.. (2016). Structural insight in HDAC-6 inhibition: Molecular docking studies of naphthalimide based HDAC inhibitors. in COST Action CM1406 EpichemBio (Epigenetic Chemical Biology), 15-16 September 2016, Groningen, Netherlands.
https://hdl.handle.net/21.15107/rcub_farfar_4943

Ružić D, Nikolić K, Senćanski M, Agbaba D, Ganesan A. Structural insight in HDAC-6 inhibition: Molecular docking studies of naphthalimide based HDAC inhibitors. in COST Action CM1406 EpichemBio (Epigenetic Chemical Biology), 15-16 September 2016, Groningen, Netherlands. 2016;.
https://hdl.handle.net/21.15107/rcub_farfar_4943 .

Ružić, Dušan, Nikolić, Katarina, Senćanski, Milan, Agbaba, Danica, Ganesan, A., "Structural insight in HDAC-6 inhibition: Molecular docking studies of naphthalimide based HDAC inhibitors" in COST Action CM1406 EpichemBio (Epigenetic Chemical Biology), 15-16 September 2016, Groningen, Netherlands (2016),
https://hdl.handle.net/21.15107/rcub_farfar_4943 .

TY  - CONF
AU  - Ružić, Dušan
AU  - Nikolić, Katarina
AU  - Agbaba, Danica
AU  - Ganesan, A.
PY  - 2016
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/5028
AB  - Histone deacetylases (HDACs) are epigenetic erasers, which are considered as transcriptional repressors and potent anticancer targets. Today, 18 human HDACs are identified and divided in four classes. FDA has approved four Histone Deacetylase Inhibitors (HDACi), defined as pan-HDAC inhibitors...
PB  - Freiburg Institute for Advanced Studies
C3  - 3rd Freiburg Epigenetic Spring Meeting and COST Action EpiChemBio CM1406, Freiburg, April 10-13
T1  - Computer aided drug design – a step closer to selective HDAC-6 inhibitor?
UR  - https://hdl.handle.net/21.15107/rcub_farfar_5028
ER  - 

@conference{
author = "Ružić, Dušan and Nikolić, Katarina and Agbaba, Danica and Ganesan, A.",
year = "2016",
abstract = "Histone deacetylases (HDACs) are epigenetic erasers, which are considered as transcriptional repressors and potent anticancer targets. Today, 18 human HDACs are identified and divided in four classes. FDA has approved four Histone Deacetylase Inhibitors (HDACi), defined as pan-HDAC inhibitors...",
publisher = "Freiburg Institute for Advanced Studies",
journal = "3rd Freiburg Epigenetic Spring Meeting and COST Action EpiChemBio CM1406, Freiburg, April 10-13",
title = "Computer aided drug design – a step closer to selective HDAC-6 inhibitor?",
url = "https://hdl.handle.net/21.15107/rcub_farfar_5028"
}

Ružić, D., Nikolić, K., Agbaba, D.,& Ganesan, A.. (2016). Computer aided drug design – a step closer to selective HDAC-6 inhibitor?. in 3rd Freiburg Epigenetic Spring Meeting and COST Action EpiChemBio CM1406, Freiburg, April 10-13
Freiburg Institute for Advanced Studies..
https://hdl.handle.net/21.15107/rcub_farfar_5028

Ružić D, Nikolić K, Agbaba D, Ganesan A. Computer aided drug design – a step closer to selective HDAC-6 inhibitor?. in 3rd Freiburg Epigenetic Spring Meeting and COST Action EpiChemBio CM1406, Freiburg, April 10-13. 2016;.
https://hdl.handle.net/21.15107/rcub_farfar_5028 .

Ružić, Dušan, Nikolić, Katarina, Agbaba, Danica, Ganesan, A., "Computer aided drug design – a step closer to selective HDAC-6 inhibitor?" in 3rd Freiburg Epigenetic Spring Meeting and COST Action EpiChemBio CM1406, Freiburg, April 10-13 (2016),
https://hdl.handle.net/21.15107/rcub_farfar_5028 .

TY  - CONF
AU  - Ružić, Dušan
AU  - Nikolić, Katarina
AU  - Agbaba, Danica
AU  - Ganesan, A.
PY  - 2016
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/4940
C3  - ISC and Alumni Symposium, Department of Biophysical Chemistry, Max Planck University, Goettingen, Germany, 19. 08. 2016
T1  - Molecular modelling - A step closer to selective histone deacetylase 6 inhibitor?
SP  - 15
EP  - 15
UR  - https://hdl.handle.net/21.15107/rcub_farfar_4940
ER  - 

@conference{
author = "Ružić, Dušan and Nikolić, Katarina and Agbaba, Danica and Ganesan, A.",
year = "2016",
journal = "ISC and Alumni Symposium, Department of Biophysical Chemistry, Max Planck University, Goettingen, Germany, 19. 08. 2016",
title = "Molecular modelling - A step closer to selective histone deacetylase 6 inhibitor?",
pages = "15-15",
url = "https://hdl.handle.net/21.15107/rcub_farfar_4940"
}

Ružić, D., Nikolić, K., Agbaba, D.,& Ganesan, A.. (2016). Molecular modelling - A step closer to selective histone deacetylase 6 inhibitor?. in ISC and Alumni Symposium, Department of Biophysical Chemistry, Max Planck University, Goettingen, Germany, 19. 08. 2016, 15-15.
https://hdl.handle.net/21.15107/rcub_farfar_4940

Ružić D, Nikolić K, Agbaba D, Ganesan A. Molecular modelling - A step closer to selective histone deacetylase 6 inhibitor?. in ISC and Alumni Symposium, Department of Biophysical Chemistry, Max Planck University, Goettingen, Germany, 19. 08. 2016. 2016;:15-15.
https://hdl.handle.net/21.15107/rcub_farfar_4940 .

Ružić, Dušan, Nikolić, Katarina, Agbaba, Danica, Ganesan, A., "Molecular modelling - A step closer to selective histone deacetylase 6 inhibitor?" in ISC and Alumni Symposium, Department of Biophysical Chemistry, Max Planck University, Goettingen, Germany, 19. 08. 2016 (2016):15-15,
https://hdl.handle.net/21.15107/rcub_farfar_4940 .