TY  - JOUR
AU  - Ranđelović, Jelena
AU  - Erić, Slavica
AU  - Savić, Vladimir
PY  - 2014
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/2222
AB  - In order to design a small molecule which potentially may interfere with CDK9/cyclin T1 complex formation and therefore influence its physiological role, a computational study of dynamics and druggability of CDK9 binding surface was conducted. Druggability estimates and pocket opening analyses indicated binding regions of cyclin T1 residues, Phe 146 and Lys 6, as starting points for the design of small molecules with the potential to inhibit the CDK9/cyclin T1 association. A pharmacophore model was created, based on these two residues and used to select potential inhibitor structures. Binding energies of the inhibitors were estimated with MM-GBSA. A good correlation of MM-GBSA energies and FTMap druggability predictions was observed. Amongst studied compounds a derivative of 2-amino-8-hydroxyquinoline was identified as the best potential candidate to inhibit CDK9/cyclin T1 interactions. 2014 Elsevier Inc. All rights reserved.
PB  - Elsevier Science Inc, New York
T2  - Journal of Molecular Graphics & Modelling
T1  - In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction
VL  - 50
SP  - 100
EP  - 112
DO  - 10.1016/j.jmgm.2014.04.002
ER  - 

@article{
author = "Ranđelović, Jelena and Erić, Slavica and Savić, Vladimir",
year = "2014",
abstract = "In order to design a small molecule which potentially may interfere with CDK9/cyclin T1 complex formation and therefore influence its physiological role, a computational study of dynamics and druggability of CDK9 binding surface was conducted. Druggability estimates and pocket opening analyses indicated binding regions of cyclin T1 residues, Phe 146 and Lys 6, as starting points for the design of small molecules with the potential to inhibit the CDK9/cyclin T1 association. A pharmacophore model was created, based on these two residues and used to select potential inhibitor structures. Binding energies of the inhibitors were estimated with MM-GBSA. A good correlation of MM-GBSA energies and FTMap druggability predictions was observed. Amongst studied compounds a derivative of 2-amino-8-hydroxyquinoline was identified as the best potential candidate to inhibit CDK9/cyclin T1 interactions. 2014 Elsevier Inc. All rights reserved.",
publisher = "Elsevier Science Inc, New York",
journal = "Journal of Molecular Graphics & Modelling",
title = "In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction",
volume = "50",
pages = "100-112",
doi = "10.1016/j.jmgm.2014.04.002"
}

Ranđelović, J., Erić, S.,& Savić, V.. (2014). In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction. in Journal of Molecular Graphics & Modelling
Elsevier Science Inc, New York., 50, 100-112.
https://doi.org/10.1016/j.jmgm.2014.04.002

Ranđelović J, Erić S, Savić V. In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction. in Journal of Molecular Graphics & Modelling. 2014;50:100-112.
doi:10.1016/j.jmgm.2014.04.002 .

Ranđelović, Jelena, Erić, Slavica, Savić, Vladimir, "In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction" in Journal of Molecular Graphics & Modelling, 50 (2014):100-112,
https://doi.org/10.1016/j.jmgm.2014.04.002 . .

TY  - JOUR
AU  - Ranđelović, Jelena
AU  - Erić, Slavica
AU  - Savić, Vladimir
PY  - 2013
UR  - https://farfar.pharmacy.bg.ac.rs/handle/123456789/1929
AB  - Cyclin dependent kinase 9 (CDK9) is a protein that belongs to the cyclin-dependent kinases family, and its main role is in the regulation of the cell transcription processes. Since the increased activity of CDK9 is connected with the development of pathological processes such as tumor growth and survival and HIV-1 replication, inhibition of the CDK9 could be of particular interest for treating such diseases. The activation of CDK9 is initiated by the formation of CDK9/cyclin T1 complex, therefore disruption of its formation could be a promising strategy for the design of CDK9 inhibitors. In order to assist in the design of potential inhibitors of CDK9/cyclin T1 complex formation, a computational study of the CDK9/cyclin T1 interface was conducted. Ten peptides were designed using the information from the analysis of the complex, hot spot residues and fragment based design. The designed peptides were docked to CDK9 structures obtained by molecular dynamics simulations of CDK9/cyclin T1 complex and the CDK9 alone and their binding affinities were evaluated using molecular mechanics Poisson Boltzman surface area (MM-PBSA) method and steered molecular dynamics (SMD). Designed peptide sequences LQTLGF and ESIILQ, both derived from the surface of cyclin T1, as well as the peptide sequence PRWPE, derived from fragment based design, showed the most favorable binding properties and were selected for our further studies.
PB  - Springer, New York
T2  - Journal of Molecular Modeling
T1  - Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex
VL  - 19
IS  - 4
SP  - 1711
EP  - 1725
DO  - 10.1007/s00894-012-1735-2
ER  - 

@article{
author = "Ranđelović, Jelena and Erić, Slavica and Savić, Vladimir",
year = "2013",
abstract = "Cyclin dependent kinase 9 (CDK9) is a protein that belongs to the cyclin-dependent kinases family, and its main role is in the regulation of the cell transcription processes. Since the increased activity of CDK9 is connected with the development of pathological processes such as tumor growth and survival and HIV-1 replication, inhibition of the CDK9 could be of particular interest for treating such diseases. The activation of CDK9 is initiated by the formation of CDK9/cyclin T1 complex, therefore disruption of its formation could be a promising strategy for the design of CDK9 inhibitors. In order to assist in the design of potential inhibitors of CDK9/cyclin T1 complex formation, a computational study of the CDK9/cyclin T1 interface was conducted. Ten peptides were designed using the information from the analysis of the complex, hot spot residues and fragment based design. The designed peptides were docked to CDK9 structures obtained by molecular dynamics simulations of CDK9/cyclin T1 complex and the CDK9 alone and their binding affinities were evaluated using molecular mechanics Poisson Boltzman surface area (MM-PBSA) method and steered molecular dynamics (SMD). Designed peptide sequences LQTLGF and ESIILQ, both derived from the surface of cyclin T1, as well as the peptide sequence PRWPE, derived from fragment based design, showed the most favorable binding properties and were selected for our further studies.",
publisher = "Springer, New York",
journal = "Journal of Molecular Modeling",
title = "Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex",
volume = "19",
number = "4",
pages = "1711-1725",
doi = "10.1007/s00894-012-1735-2"
}

Ranđelović, J., Erić, S.,& Savić, V.. (2013). Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex. in Journal of Molecular Modeling
Springer, New York., 19(4), 1711-1725.
https://doi.org/10.1007/s00894-012-1735-2

Ranđelović J, Erić S, Savić V. Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex. in Journal of Molecular Modeling. 2013;19(4):1711-1725.
doi:10.1007/s00894-012-1735-2 .

Ranđelović, Jelena, Erić, Slavica, Savić, Vladimir, "Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex" in Journal of Molecular Modeling, 19, no. 4 (2013):1711-1725,
https://doi.org/10.1007/s00894-012-1735-2 . .