Chirality, Alzheimer's Disease, and Amyloid Beta.


Chirality is of para­mount im­por­tance to all living systems. It is a property of all principal bio­mo­le­cular buil­ding blocks, i.e., amino acids except glycine, sugars and nucleosides, as well as lipids. Continuous improvement of preparative metho­dologies meanwhile allows increasingly complex mole­cules to be synthesized, which includes so­phi­s­ti­ca­ted mirror-image biomolecules, such as proteins.

Aggregation-prone (amyloidogenic) polypeptides are produced by living systems, often as cleavage products of substantially larger protein precursors. Whereas their functions in health are challenging to study and not always well understood, it is widely accepted that an imbalance between their production and clearance can trigger a range of pathological conditions, including Alzheimer’s Disease (AD / amyloid β, Aβ), Huntington’s Disease (HD / the huntingtin protein) and Type 2 Diabetes (T2D / amylin). A feature that is common to all those peptides is the high polydispersity across both aggregate size and shape, with distinctions frequently made between oligomers, protofibrils and fibrils. In sporadic AD, Aβ oligomers (especially those derived from the 42-amino acid long isoform, Aβ42) are believed to be particularly harmful, whereas fibrils appear to represent an aggregation endpoint that may be relatively benign.

Peptide backbone conformations can be altered through introduction of D-amino acids (“Chiral Editing”), and replacement of L- by D-amino acids across the entire peptide yields mirror image (“D-“)Aβ. Because of the enantiomeric relation, D-Aβ has to possess an identical oligomer-pro­to­fibril-fibril distribution to that of the natural (“L-“) stereoisomer. However, all 3D-structural para­meters are mirrored in D-Aβ42, including the peptide backbone. Through stereochemical argu­ments, we envisioned that racemic Aβ42 should exhibit increased fibril formation and reduced toxicity. We synthesized the two enantiomers of Aβ42 and found that their equimolar mixture exhibited pronounced acceleration of fibril formation, as compared to the enantiopure coun­ter­parts. This led to substantial suppression of oligomer formation and inhibition of toxicity in model cell-based systems. We termed this the “Chiral Inactivation” effect. The underlying molecular mechanisms that lead to the differences in biophysical and biological properties observed between enantiopure and racemic Aβ42 remain subject of active research in our laboratory.

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 "Memory is our ability to predict things which have already happened."

 - Jevgenij Raskatov

Keynote & Welcome to Academia

Our methods.

Synthesis and biophysical characterization:


Every project in the lab begins with organic synthesis, and we employ methods, including classical organic chemistry transformations, (asymmetric) transition-metal catalyzed chemistry, and microwave-assisted poly­peptide synthesis. We then systematically probe the molecular frameworks created, employing quantitative biophysical and physical organic methods. Those include nuclear magnetic resonance (N.B. UCSC received a brand new 800 MHz instrument in May 2016) circular dichroism, dynamic light scattering, isothermal titration calorimetry and small-angle X-ray scattering (SLAC facilities, Stanford). We benefit greatly from the existence of the state-of-the-art screening center at UCSC, and collaborate with the Ayzner lab on synchrotron-related experiments.

Biology:


Molecules that show interesting properties in cell-free systems are studied in the biologically relevant setting. Neurodegeneration being a major area of interest for the lab, we focus our cell culture studies mostly on brain cells – neurons and astrocytes. Neuroinflammation constitutes a major contribution to neurodegenerative disorders, and the crosstalk with the immune system, including Nuclear Factor Kappa B signaling, hence, also of high interest. We furthermore collaborate with electrophysiologists to elucidate molecular mechanisms of action of the compounds we synthesize, in hippocampal slices (long-term potentiation experiments).

Computation:


We employ density functional theory, as well as molecular dynamics simulations to gain deeper insight into structural and functional properties of the frameworks under investigation. The continuous crosstalk between experiment and theory gives rise to an intellectually stimulating environment with great learning opportunities for the students. Computational work is typically performed by Prof. Raskatov himself, but highly motivated students are encouraged to inquire.