Riassunto analitico
Histone deacetylase 6 (HDAC6) is a member of HDAC family composed by enzymes primarily involved in the deacetylation of histones. HDAC6 is the best characterized member of class IIb and it is unique in that it is predominantly cytosolic and partecipates in the deacetylation of non-histone proteins, such as α-tubulin and Hsp90. HDAC6 modulates the acetylation of non-histone regulatory proteins implicated in cancer relevant processes, including cell migration, metastasis, angiogenesis and stress-response pathways. For this reason HDAC6 is an attractive target in cancer research.
To overcome known problems linked to chemotherapy, a number of strategies have been tested, including combination therapies and multitarget inhibitors. Polypharmacology, which consists in the use of a single drug able to inhibit multiple biological targets, is becoming an increasingly important approach in drug design and discovery. This choice is justified by several potential advantages of multi-target drugs over single-targeted or combination therapies, including concurrent pharmacokinetics, minimized off-target adverse effects, and drug-drug interactions caused by multiple agents, as well as increased patiente compliance.
HDAC6 and Hsp90 are both validated targets in cancer. These targets are intimately biologically linked. In fact, since Hsp90 is a substrate of HDAC6, inhibition of HDAC6 leads to the accumulation of acetylated Hsp90, resulting in loss of biological function of the chaperone Hsp90 and loss of its ability to bind client proteins implicated in signal transduction and cell-cycle control.
Inhibitors of HDAC6 and inhibitors of Hsp90 are currently in clinical trials. Recent studies have evaluated combination therapies, and showed that a combination of Hsp90 and HDAC6 inhibitors lead to synergistic effects. Because of the strong relationship between Hsp90 and HDAC6 functions and the synergistic effects demonstrated by their respective inhibitors, the discovery of potential dual Hsp90/HDAC6 inhibitors is a highly desirable goal.
The aim of this research is the design of dual inhibitors of Hsp90 and HDAC6 by means of virtual screening techniques. In particular, my work was focused on HDAC6. Since a crystallographic structure of human HDAC6 is not yet available, an homology model of HDAC6 was generated using MODELLER software. This model was then used to perform an Induced Fit Docking of known HDAC6 inhibitors in the putative Zinc-binding site, leading to a total of six HDAC6 conformations able to accomodate these ligands with favourable scores. A virtual screening (VS) of commercially-available compounds into these six HDAC6 models was then performed. To this end, ~600.000 molecules from the Asinex collection were downloaded from the ZINC database and docked into the six HDAC6 structures by using the Glide program. At the same time, a similar VS approach based on four Hsp90 structures was conducted by a colleague in the same research group. The output of VS for every structure of HDAC6 was subjected to two consecutive steps of filtering, the first to eliminate molecules that did not coordinate the zinc ion, the second to eliminate molecules bearing a carboxylate group as a zinc binding group, these molecules being known ligands with scarce activity and generally poor ADME properties. Molecules filtered and ranked according to GlideScore were then post-processed using the BEAR program developed in the laboratory. Finally, the VS results obtained on the six conformations of HDAC6 were crossed with the VS results obtained on the four conformations of Hsp90, leading to twenty-four ranked lists containing potential dual ligands. After visual inspection of the best-ranking complexes, a selection of compounds with high scores and favourable active site interactions with both proteins was finally made. These compounds will be tested at the National Cancer Institute (NCI, USA), thanks to a collaboration established with Dr. Len Neckers.
|
Abstract
Histone deacetylase 6 (HDAC6) is a member of HDAC family composed by enzymes primarily involved in the deacetylation of histones. HDAC6 is the best characterized member of class IIb and it is unique in that it is predominantly cytosolic and partecipates in the deacetylation of non-histone proteins, such as α-tubulin and Hsp90. HDAC6 modulates the acetylation of non-histone regulatory proteins implicated in cancer relevant processes, including cell migration, metastasis, angiogenesis and stress-response pathways. For this reason HDAC6 is an attractive target in cancer research.
To overcome known problems linked to chemotherapy, a number of strategies have been tested, including combination therapies and multitarget inhibitors. Polypharmacology, which consists in the use of a single drug able to inhibit multiple biological targets, is becoming an increasingly important approach in drug design and discovery. This choice is justified by several potential advantages of multi-target drugs over single-targeted or combination therapies, including concurrent pharmacokinetics, minimized off-target adverse effects, and drug-drug interactions caused by multiple agents, as well as increased patiente compliance.
HDAC6 and Hsp90 are both validated targets in cancer. These targets are intimately biologically linked. In fact, since Hsp90 is a substrate of HDAC6, inhibition of HDAC6 leads to the accumulation of acetylated Hsp90, resulting in loss of biological function of the chaperone Hsp90 and loss of its ability to bind client proteins implicated in signal transduction and cell-cycle control.
Inhibitors of HDAC6 and inhibitors of Hsp90 are currently in clinical trials. Recent studies have evaluated combination therapies, and showed that a combination of Hsp90 and HDAC6 inhibitors lead to synergistic effects. Because of the strong relationship between Hsp90 and HDAC6 functions and the synergistic effects demonstrated by their respective inhibitors, the discovery of potential dual Hsp90/HDAC6 inhibitors is a highly desirable goal.
The aim of this research is the design of dual inhibitors of Hsp90 and HDAC6 by means of virtual screening techniques. In particular, my work was focused on HDAC6. Since a crystallographic structure of human HDAC6 is not yet available, an homology model of HDAC6 was generated using MODELLER software. This model was then used to perform an Induced Fit Docking of known HDAC6 inhibitors in the putative Zinc-binding site, leading to a total of six HDAC6 conformations able to accomodate these ligands with favourable scores. A virtual screening (VS) of commercially-available compounds into these six HDAC6 models was then performed. To this end, ~600.000 molecules from the Asinex collection were downloaded from the ZINC database and docked into the six HDAC6 structures by using the Glide program. At the same time, a similar VS approach based on four Hsp90 structures was conducted by a colleague in the same research group. The output of VS for every structure of HDAC6 was subjected to two consecutive steps of filtering, the first to eliminate molecules that did not coordinate the zinc ion, the second to eliminate molecules bearing a carboxylate group as a zinc binding group, these molecules being known ligands with scarce activity and generally poor ADME properties. Molecules filtered and ranked according to GlideScore were then post-processed using the BEAR program developed in the laboratory. Finally, the VS results obtained on the six conformations of HDAC6 were crossed with the VS results obtained on the four conformations of Hsp90, leading to twenty-four ranked lists containing potential dual ligands. After visual inspection of the best-ranking complexes, a selection of compounds with high scores and favourable active site interactions with both proteins was finally made. These compounds will be tested at the National Cancer Institute (NCI, USA), thanks to a collaboration established with Dr. Len Neckers.
|
