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Institute for Advanced Simulations (IAS)

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Neurodegenerative diseases

Parkinson’s disease

Parkinson’s disease (PD) is a degenerative disorder of the central nervous system, which affects ~2% of the population over 65 years in the western countries. In PD, the progressive damage of dopaminergic neurons in the substantia nigra leads to substantial reduction in the dopamine concentration in striatum. This reduction is related with tremor, akinesia/bradykinesia, rigidity and postural instability.

A2A adenosine receptor antagonists are promising agents for the treatment of PD. The intake of one of them, caffeine, is positively associated with a reduced risk of PD. Elucidating the mechanism of caffeine binding with A2A receptor at molecular level is of great importance in designing anti-PD drug with high selectivity and affinity. Here, we are developing molecular models of caffeine-derived ligand targeting A2A receptor using multi-scale molecular simulation. The work is in collaboration with Prof. A. Bauer, in the FZJ campus.

A2AR/Caffeine complexFigure 1 - Multiscale simulation of the A2AR-caffeine complex: The backbone of the protein is represented with a coarse-grain method, while the binding site along with its hydration sphere with all-atom methods.

α-synuclein (AS) is an intrinsically disordered protein associated with the pathogenesis of PD. It is the main component of Lewy bodies' plaques forming the brains of patients suffering from the disease.
Multidimensional heteronuclear NMR spectroscopy provides valuable structural information on adducts between naturally unfolded proteins and their ligands. These are often of high pharmacological relevance. Unfortunately, the determination of the contributions to observe chemical shifts changes upon ligand binding is challenging.
We have developed a tool that uses molecular dynamics (MD) trajectories to help interpret 2D NMR data of intrinsically disordered proteins. We apply this tool to AS interacting with dopamine (DOP), an inhibitor of fibril formation, and with its oxidation products in water solution (Fig. 2). DOP binds preferentially to 125YEMPS129 residues in the C-terminal and, to few residues of the so-called NAC region, consistently with experimental data. Our tool provides a rationale for the observed changes in chemical shifts (Δcs) upon binding in terms of direct contacts with the ligand and conformational changes of the protein.

Alpha-synuclein/dopamineFigure 2 – Alpha-synuclein interacting with dopamine, an inhibitor of fibril formation.

Prion diseases

Prion diseases, or transmissible spongiform encephalopathies (TSEs), are rare fatal neurodegenerative disorders. The key event in these maladies is the posttranslational conversion of the ubiquitously expressed cellular form of the prion protein (PrPC) into the misfolded pathogenic isoform, PrPSc or prions. About 15% of human (Hu) TSEs are inherited, caused by so far identified 58 pathogenic mutations (PMs) in the gene encoding for HuPrPC. The PMs are located all over the protein: most of them in the folded C-terminal globular domain (GD), and few in the disordered N-terminal domain (N-term).
For the structured globular domain of the protein, we applied all-atom molecular dynamics simulations in explicit solvent (Rossetti, G., et al. (2010). Proteins, 78(16), 3270–3280. Rossetti, G., et al. (2011). J. Mol. Bio., 411(3), 700–712.). For the intrinsically disordered domain, we employed a powerful Monte Carlo simulation approach, PROFASI, developed in our campus by Dr. Sandipan Mohanty in the Jülich Supercomputing Center (Cong, X. et al. (2013) J. Chem. Theory and Comput. 9, 5158-5167). Our work discovered that the mutations in the structured domain destabilize the native fold of the protein in two specific regions, which are likely the “hot spots” of the protein. This suggests that the early stage of the prion protein misfolding involves the two identified hot spots, which may serve as molecular targets for antiprion drug design. Those in the disordered domain affect, in a subtle manner, the regions responsible for binding cellular partners and/or for the protein biosynthesis. Thus, they may cause prion diseases by altering the protein’s physiological function and/or its biosynthesis. The findings may have broad implications in the pathogenic protein-misfolding problem that commonly occurs in neurodegenerative diseases such as Alzheimer’s disease. Most importantly, our simulation results turned out to be consistent with all of the available experimental data.

N-term_MoPrPCFigure 3 - The ensemble of conformations of N-term_MoPrPC predicted using REMC simulations

Alzheimer’s disease

Alzheimer’s disease (AD) is one of the most common neurodegenerative diseases. An important characteristic in the pathogenesis of AD is the dyshomeostasis of metal ions, mainly Zn(II) and Ca(II) ions, in glutamatergic neurons. It is believed that Zn(II) promotes formation of amyloid plaques of Aβ peptide, which is one of the main features of the disease. Formation of the Aβ plaques subtracts Zn(II) from the ion pool, which at the same time causes unbalance of homeostasis of Ca(II) and other metal ions. In collaboration with Prof. K. Amunts in our campus and Prof. S. Sensi from Department of Neurology and Farmacology, University of California at Irvine (USA) we are designing a highly specific Zn(II) transporter on the basis of dipeptide L-carnosine to alter zinc concentrations in neurons.
The other way of regulation of ion pool inside and outside of the cell is by acting on ion channels, such as NMDA and AMPA receptors. NMDA receptor is blocked in a voltage dependent manner by Mg2+, a blockade that is relieved by Na+ ions flow through AMPA receptor causing a depolarization of the membrane. This allows Na+, K+, and Ca2+ ions to flow through the channel. We plan to use rational drug design technique in order to design new compounds able to activate AMPA receptor.

Huntington disease

Huntington disease (HD) 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 huntingtin (Htt). HD penetrance is correlated to the number n of CAG repeats (the disease threshold is n=36). HTT mRNA transcripts with n above threshold (RNACAG) may contribute to the pathogenesis, aberrantly regulate several cellular mechanisms and bind to proteins to form pathological complexes, such that between the Midline-1 protein in complex and the phosphatase 2A (Fig 4A). Building on extensive modeling work on well-known RNA structures here we are identifying novel ligands targeting specifically RNACAG that may affect the formation of such complex, hence reducing the overexpression of aberrant Htt protein (Krauβ et al. (2013) Nature). The work is in collaboration with Dr. Sybille Krauβ at the German Center for Neurodegenerative Diseases in Bonn.

HuntingtonFigure 4 - The translation of expanded CAG repeats mRNAs is regulated by the MID1 protein complex. The MID1 protein mediates the binding of the translational regulator S6K to expanded CAG repeats. PP2A and the mammalian target rapamycin (mTOR) control the phosphodependent activity of S6K. MID1 is an inducer of mTOR and an inhibitor of PP2A and, therefore, indirectly stimulates translation via S6K.