Ongoing Projects
Recapitulation of bona fide Alzheimer-like tau fibrils from brain homogenates
Recreating true Alzheimer-like tau amyloids remains a topic of interest for studying their unique propagation cascade, for using them as libraries of seeds for animal and cellular studies, and for inhibiting their growth. A collaboration between the centre for misfolding diseases, and the laboratory of molecular biology zeroes in on a method for faithful propagation. Through several iterative rounds of tau constructs including truncated and 0N3R tau, we arrive at a near perfect recapitulation of the AD tau conformer. Manuscript in preparation
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Overlay of ex-vivo alzheimer tau fibrils (grey, Fitzpatrick, Nature 2017) with our amplified 0N3R AD-seeded recombinant tau fibrils (beige)
Conformer-specific kinetics of tau aggregation
A project birthed out of COVID lockdown boredom: sifting through old aggregation data led us to uncover distinct aggregation profiles of tau substrates seeded with different brain homogenates. We show with this work that the aggregation cascade of 5 tau conformers (AD, PiD, PSP, CBD, GGT type III) have unique sub-molecular steps. Many are dominated by fragmentation events, while others exhibit saturating and competing kinetic steps. We believe this work highlights the need for conformer-specific aggregation assays in order to target specific aggregates with small molecule inihbitors. It may also unearth divergent mechanisms of cellular propagation. Manuscript in preparation
Cartoonization of primary steps in amyloidogenesis and propagation. Histograms represent relative contributions of each molecular step to the propagation of conformers studied in this work.
Kinetic-informed machine learning identification of conformer-specific tau aggregation inhibitors
Using cryo-EM structures of AD tau fibrils, we docked over 5 million molecules to a known hydrophobic surface moiety necessary for AD tau seed propagation. With development of a careful conformer-specific kinetic aggregation assay, specific sub-molecular steps were targeted for inhibition through iterative roudns of machine learning. We identified several ultra-potent tau aggregation inhibitors that showed specificity for AD, and no such aggregation inhibition for PiD tau aggregation. This work highlights the power of aggregation kinetics in drug discovery. Manuscript submitted to Nature Communications
Top: leading candidate small molecule inhibitors of AD-tau amyloid formation discovered through iterative kinetic-informed machine learning; Bottom: example kinetic profiles showing unique inhibited steps
Unified seeding method for amplification of tau aggregates using two recombinant substrates
Tau aggregates take two basic classifications - those that are composed of tau isoforms containing all four microtubule binding repeats (4R), and those that contain only three (3R). As the structures of the ex vivo aggregates are solved by cryo-EM, methods for their amplification and faithful propagation can be honed with careful substrate design. We previously had success amplifying AD and PiD tau with a singular 3R substrate where fluorescence output distinguished strains perfectly. This work creates a dichotomous key with a new substrate, K11, capable of discriminating 4R tau strains in a similar fashion. Manuscript in preparation
A unified dichotomous key for the seed-based diagnosis of tauopathy specimens using recombinant 3R (K12) and 4R (K11) tau substrates
An unmet need - ultrasensitive detection of systemic amyloids from biospecimens
Systemic amyloidosis is a rapidly progressive disease characterized by fibril buildup in end-organs, especially the kidneys, heart, and liver. At the time of diagnosis, there is significant deposition of amyloid causing end-organ failure, prompting clinicians to biopsy. The diagnosis hinges on enough material to be detectable through bulk measurements - amyloid-specific stains like congo Red, or through mass spectrometric methods. It is now clear that light chain amyloids adopt multiple conformers which are dictated in part by mutations. I am interested in designing a universal light chain amyloid capable of amplifying AL amyloids from crude biospecimens, which may provide diagnosis prior to end-organ damage. Structures on the right taken from (Sara Karimi-Farsijani Nat Comm 2024) Seeking collaborators and funding
Left: unique AL amyloid structures solved by cryo-EM (Sara Karimi-Farsijani 2024). Right: design of universal AL substrate can enable sensitive detection of AL amyloids from crude biospecimens with strain discrimination