Neurodegenerative diseases
Many neurodegenerative diseases are associated with the accumulation of fibrillar proteins. The unifying features of a fibril formation is the structural transition from an initial globular or intrinsically disordered state to a β-structural form. Using molecular simulations we try to understand how the presence of ligands affect the structural stability of proteins undergoing fibrillation in Parkinson’s, Prion diseases and Hungtinton. Our calculations may help identify compounds which affect fibrillation as well as uncover the role of specific cellular partners for protein fibrillation.
Prion diseases (Collaboration with G. Legname Lab, SISSA, Trieste)
Prion protein. - These are associated with the accumulation of a misfolded isoform (PrPsc) of the prion protein PrPc. Interfering with the conversion of PrPc into PrPsc is a powerful strategy for pharmaceutical intervention. An excellent strategy is based on the design of ligands stabilizing the PrPc. Unfortunately, however, in silico design of ligands targeting proteins undergoing fibrillation in neurodegenerative diseases, such as prion protein, is difficult due to the lack of deep binding pockets in these proteins and due to the paucity of 3D information of ligand-target complexes. We have established a computational approach that combines standard docking methods with molecular dynamics and free energy simulations in explicit solvent to address this issue in the context of prion protein. The protocol was tested on the known anti-prion compound (GN8), and compared with experimental data. It turns out that the combination of the three methods of the protocol is necessary to satisfy contacts experimentally detected by NMR spectroscopy. In addition, this approach allows to estimate the binding free energy.
In collaboration with the medicinal chemistry groups of Maria Laura Bolognesi, we are designing ligands interfering with prion fibrillation and look at their binding mode using our computational protocol.
Parkinson's disease (Collaboration with G. Legname and S. Gustincich Labs, SISSA, Trieste)
α-synuclein is the major component of Parikinson’s Lewy bodies, which have been proposed to play a role for the disease. Dopamine and its oxidation derivatives may inhibit the α-synuclein aggregation by non-covalent binding. Exploiting this fact, we applied an integrated computational and experimental approach to find alternative ligands that might modulate the fibrillization of α-synuclein. Ligands structurally and electrostatically similar to dopamine were screened from an established library (collaboration with S. Gustincich, G. Legname.
Five analogs were selected for in vitro experimentation from the similarity ranked list of analogs. Molecular dynamics simulations showed they were, like dopamine, binding non-covalently to α-synuclein and, although much weaker than dopamine, they shared some of its binding properties. In vitro fibrillization assays were performed on these five dopamine analogs. Consistent with our predictions, analyses by atomic force and transmission electron microscopy revealed that all of the selected ligands affected the aggregation process, albeit to a varying and lesser extent than dopamine, used as the control ligand. The in silico / in vitro approach presented here emerges as a possible strategy for identifying ligands interfering with such a complex process.
Copper and α-synuclein. - Elevated Cu concentrations have been reported in the cerebrospinal fluid of Parkinson’s disease patients. In addition, individuals with chronic industrial exposure to Cu have an increased rate of Parkinson’s disease. Cu(II) ions have been shown to bind α-synuclein and accelerate kinetics of fibrillation in vitro.
In collaboration with C. O. Fernandez we are providing structural models of the way copper binds to the protein.
We are performing a structural prediction of a complex between F-actin and the N-terminal part of mut-Htt, which it is proposed to bind F-actin and to trigger cell apoptosis. This may play an important role in determining the aggregation potential of mut-Htt in cells (Shao, J.; Welch, W. J.; Di Prospero, N. A.; Diamond, M. I., Mol. Cell. Biol. 28 (17), 5196‐5208 (2008)).
N17-Huntintin: interactions with molecular partners (Collaboration with Prof. M. Diamond)
Huntington disease is a neurodegenerative disorder producing motor, cognitive and psychiatric symptoms. It is caused by a trinucleotide CAG repeat gene mutations, encoding an expanded polyglutamine (polyQ) tract in the respective protein. Proteolytic processing of mut-Htt lead to the formation of short N-terminal polyQ-containing fragments that have the propensity to aggregate and cause neurodegeneration. These fragments form insoluble β-sheet aggregates that are the hallmark of the disease.
We are performing a structural prediction of a complex between F-actin and the N-terminal part of mut-Htt, which it is proposed to bind F-actin and to trigger cell apoptosis. This may play an important role in determining the aggregation potential of mut-Htt in cells (Shao, J.; Welch, W. J.; Di Prospero, N. A.; Diamond, M. I., Mol. Cell. Biol. 28 (17), 5196‐5208 (2008)).