(415b) Computational Analysis of Photophysical Changes of Oligomeric P-Phenylene Ethynylene upon Binding to Amyloid-? Aggregates

Alzheimer’s disease is an uncurable progressive neurodegenerative disease and is the most common cause of dementia. As current understanding of the disease suggests damage begins accumulating a decade before diagnosable symptoms, preventative treatment strategies will require screenings in absence of symptoms. The high cost of PET and MRI scans make them unsuitable for the throughput necessary to screen the large population of 65+ individuals most at risk of developing Alzheimer’s disease. An alternative method is near-IR fluorescence imaging, with a lower cost and a less invasive procedure. We have reported a small-molecule fluorescent sensor able to selectively detect and oxidize the amyloid-β oligomers implied as pathogenic agents in the early development of Alzheimer's disease. In this study, we use computational modeling to gain a greater understanding of what changes in molecule-protein binding lead to both turn-on fluorescence and turn-on singlet oxygen generation.

Methodology

We utilize all-atom molecular dynamics to model fluorophore molecule behavior in environments of interest. These environments being a singular monomer, a dimer, and a dimer associated with the surface of an amyloid-β aggregate. We first extract dihedral angles associated with the conjugated pi-system backbone to measure the overall planarity of the fluorophores. We also periodically extract snapshots of molecular conformation upon which we perform density functional theory and time-dependent density functional theory ab initio calculations. These calculations are used to obtain vertical excitation energies and oscillator strengths for said transitions, from which we can gain an understanding over the absorbance behavior of the fluorophores in these conditions. We further use transition density cube calculations to compute the impact of Coulombic coupling interactions upon dimer excitation energies. These computations are compared against experimental spectra.

Results and Conclusions

The planarity of the fluorophore’s chromatophore backbone is controlled by rotation around two triple bonds, in turn forming two dihedral angles. For the monomer, the full possibility space of these angles is inhabited in a random fashion. Upon dimerization, we find the molecules are restricted to only planar conformations while still being able to transition between these conformations. When further restricted by adherence to the protein aggregate surface, the molecules retain the restriction to planar conformations, but are largely restricted from transitioning between different planar states.

The computed vertical excitations for the monomer reflect the random conformations. We define excitation to the S1 state by the lowest calculated transition with appropriate energy and non-negligible oscillator strength. For the monomer, this transition is not always available, with the lowest energy available transition being the experimental S2 transition for many out-of-plane molecular conformations. The S1 transition stabilizes upon dimerization, always being accessible and typically being the lowest energy available transition calculated. This reflects the condition’s tendency for planarity, as the molecules spend greater time in the planar conformations where the S1 transition is favored. It is yet further stabilized upon protein adherence, where for all snapshots the lowest energy computed excitation has a non-negligible oscillator and so corresponds with the S1 transition. By combining all calculated vertical transitions into a spectrum, and then combining all snapshot spectra into a single spectrum, we can create computational spectra corresponding to the bulk steady-state conditions of experimental spectra. We see a redshift and a strengthening of the S1 transition upon dimerization, and a further redshift upon protein association.

These calculations only describe how geometry changes upon dimerization alter fluorophore behavior. To expand into dimer interactions, we use the transition density cube method to calculate Coulombic interaction energies. This method assumes dimers are Kasha-like: possessing strong coupling, but without any meaningful charge-transfer states and without substantial vibronic coupling. The dimers alone show largely H-aggregate behavior, with reasonably strong transition dipoles and positive interaction energies. The dimers switch to largely J-aggregates upon association with protein, possessing negative interaction energies. These calculations suggest further redshifts and stronger absorbance upon protein adhesion.

All the computational data point to a redshift and increased S1 absorbance upon dimerization, with both strengthening upon association with protein aggregates. First through conformational changes induced by rotational restriction upon dimerization, and then through a transition from H- to J-aggregates. This behavior is reflected experimentally. The monomer form is highly disfavored in the aqueous conditions of interest for potential clinical use. However, the computed redshift and strengthened absorbance is seen experimentally upon addition of protein aggregates.

This study investigates two potential sources of increased absorbance intensities upon protein binding. Increased absorbance intensity does correlate with increased fluorescence intensity, and the conversion from H- to J-aggregates provides another suggestion for the turn-on fluorescence observed. However, future work directly analyzing emission behavior is required to gain a clear understanding of the source of observed fluorescence turn-on.