Quantum Mechanics/Molecular Mechanics Density Functional Theory Simulations of the Optical Properties Fingerprinting the Ligand-Binding of Pentameric Formyl Thiophene Acetic Acid in Amyloid-β(1–42)

Abstract

The binding pocket proposed by König König Chem. Commun.20185430303033 for the biomarker pentameric formyl thiophene acetic acid (p-FTAA) in the fibrillar structure of amyloid-β(1–42) has been put to the test by the comparison of theoretical and experimental optical absorption and fluorescence spectra obtained in a water environment and inside the protein scaffold. The optical absorption/emission properties of this luminescent conjugated oligothiophene were studied by means of classical force field molecular dynamics simulations to account for the sampling of configuration space in conjunction with polarizable embedding time-dependent density functional theory calculations of spectra. The nuclear motions of residues in the β-sheet were found to be modest, and the time dependence of embedding parameters was shown to be negligible so that a time-independent parameter set could be derived and used for all 300 snapshots considered in the spectrum averaging. In regard to linear absorption spectra, the calculated red shift due to protein binding for the dominant S 1 ← S 0 transition in p-FTAA was found to be equal to 23 nm (0.17 eV), which is in excellent agreement with the corresponding experimental result of 18 nm and taken as corroborating evidence for having correctly identified the binding pocket of p-FTAA in the amyloid. The underlying mechanisms for the calculated red shift were disentangled, and it is shown that some 20 nm (0.15 eV) of the total 23 nm (0.17 eV) is associated with increased planarity of p-FTAA in the binding pocket, whereas a mere 3 nm (0.02 eV) is associated with changes in the environment. In regard to emission spectra, we demonstrate that intersystem crossing from the excited S 1 state to the triplet manifold of states is a less likely event for p-FTAA in the binding pocket as compared to in the aqueous solution, and we thereby partly explain the much higher quantum yield of fluorescence for the more rigid p-FTAA in the binding pocket. Two-photon absorption in p-FTAA is shown to predominantly occur to an overall symmetric excited state and be more than twice as strong for the biomarker in the binding pocket as compared to in water. The corresponding red shift, on the other hand, is very small. Earlier experimental two-photon fluorescence imaging using p-FTAA is shown not to target the dominant two-photon state, and ways to reach a higher image quality (lower signal-to-noise ratio) are proposed in terms of tuning the laser wavelength toward the region of 600 nm or the synthesis of asymmetric ligands with S 1 states that are both one- and two-photon allowed.

Tau Protein Binding Modes in Alzheimer’s Disease for Cationic Luminescent Ligands

“… 26 It was later conclusively shown that the fingerprinting optical signal responses of this particular ligand binding are primarily due to an increased planarity in the π-conjugated system of the ligand. 27 , 29 There are good reasons, however, to believe that the underlying microscopic mechanisms are different in the present case, as the bTVBT4 ligand differs in several important ways—(i) it is cationic instead of anionic with a charge that is largely delocalized over the π-conjugated system instead of being localized to carboxylate side chains and (ii) the molecular structure is not as flexible due to the vinylene double bond. It is reasonable to assume that the relevant binding modes of the ligands targeting tau are found in the structurally ordered core, and we therefore adopted the cryo-EM structure as a starting point in an attempt to reveal the most important binding modes of bTVBT4.…”

“…The planarity parameter defined in ref ( 29 ) was shown to correlate well to the transition energy for anionic LCOs and be the key descriptor for the changes of optical responses of p-FTAA upon binding to Aβ. 27 For bTVBT4, this parameter changes insignificantly from 3.43 ± 0.20 in solution to 3.49 ± 0.18 in site A of tau, suggesting that the associated red shift in the absorption spectrum is primarily due to changes in the electronic structure and not molecular structure. When comparing experimental decay times of bTVBT4 in various solutions and when bound to tau aggregates in AD, it is noted that it displays strikingly longer decay times in the latter case, ranging from 1.7 to 2.4 ns; see Figure S19 in the SI .…”

“…, not changing over the course of the dynamics as the fibril is in fact quite rigid. 27 But, the ligand p-FTAA exhibits a strong Coulombic-driven binding to Aβ at fixed loci, while the bTVBT4 ligand shows movements along the fibril axis while remaining in binding site A (see Figure S13 ). We therefore approximated the PE parameters for tau not only to be time-independent but also unresponsive to the ligand interaction, i.e.…”

“… 28 − 30 We have applied this protocol to study the binding of the anionic p-FTAA ligand to amyloid-β and showed that the fingerprinting optical responses are associated with the planarity of the π-conjugated system. 27 The ligand subject of the present study, bTVBT4, belongs to the bTV category and features a cationic benzothiazole (BT) moiety, see Figure 1 . In contrast to p-FTAA, it demonstrates tau-specific binding, and a prime objective of the present study is to see whether or not this protein-specificity is possible to rationalize within the realm of our simple fibrillar models of the disease aggregates.…”

Deciphering the Electronic Transitions of Thiophene‐Based Donor‐Acceptor‐Donor Pentameric Ligands Utilized for Multimodal Fluorescence Microscopy of Protein Aggregates

“…The calculations were performed with use of the Gaussian program. Two‐photon absorption were calculated using same basis set and level of theory, with the use of the Dalton program 31 using the same procedure as described in our previous paper [32] …”