Substituent, Charge, and Size Effects on the Fluorogenic Performance of Amyloid Ligands: A Small-Library Screening Study

Abstract

Developing new molecular ligands for the direct detection and tracking of amyloid protein aggregates is key to understanding and defeating myriad neurodegenerative and other disorders including Alzheimer’s and Parkinson’s diseases. A crucial factor in the performance of an amyloid dye is its ability to detect the amyloid structural motif independent of the sequence of the amyloid-forming protomer. The current study investigates structure–function relationships of a class of novel phenyleneethynylene (PPE)-based dyes and fluorescent polymers using amyloid fibrils formed by two model proteins: lysozyme and insulin. A small library of 18 PPE compounds that vary in molecular weights, charge densities, water solubilities, and types and geometries of functional groups was tested. One compound, the small anionic oligo(p-phenylene ethynylene) electrolyte OPE1, was identified as a selective sensor for the amyloid conformation of both lysozyme and insulin. On the basis of protein binding and photophysical changes observed in the dye from this set of PPE compounds, keys to the selective detection of the amyloid protein conformation include moderate size, negative charge, and substituents that provide high microenvironment sensitivity to the fluorescence yield. These principles can serve as a guide for the further refinement of the effective amyloid-sensing molecules.

Highly Effective Inactivation of SARS-CoV-2 by Conjugated Polymers and Oligomers

“…As mentioned previously and detailed in Figure 4, anionic oligomer 1 and cationic oligomer 3 show rapid and effective inactivation of SARS-CoV-2 under irradiation with near UV light with essentially complete inactivation in 10-15 min, while anionic oligomer 2 shows much slower inactivation under the same conditions. While oligomer 2 has been shown in other studies to bind strongly to misfolded proteins and fragments, [40][41][42] it seems reasonable as 2 is more hydrophilic than 1 or 3 and better solubilized in water but less able to penetrate into the interior of the virus. The curious effect that oligomer 2 is less active than 1 may also be associated with the fact that the ester groups have been shown to give rise to rapid excited state quenching of the oligomer in water.…”

“…Quite likely, the smaller oligomers may penetrate into the interior of the virus perhaps even binding to the N-protein that is directly connected to the virus RNA. 3 Since we have shown in other studies that both negatively and positively charged OPEs can bind with misfolded proteins or protein fragments, [40][41][42] binding of the polymers and oligomers used in this study with virial proteins and subsequent generation of singlet oxygen by irradiation close to the RNA seems a likely path for virus inactivation. 18 The observation that the cationic quaternary ammonium poly-4 is inactive in the dark is a harbinger that classic quaternary ammonium surfactants may not be particularly active against the virus.…”

“…Thus, the selection of the test compounds for the pilot project was in-part based on charge: oligomers 1 and 2 are negatively charged. Moreover, oligomer 2 has been shown to associate strongly with several proteins [40][41][42] and in fact, induces protein oxidation upon irradiation. 30 The cationic polymer poly-4 has become our workhorse compound for antimicrobial work.…”

A Portrait of the OPE as a Biological Agent

“…The same group in 2017 selected a small library of OPE and PPE derivatives [ 39 ] as amyloid trackers towards another amyloid protein model bovine insulin, which, in a fashion similar to the previously studied lysozyme [ 34 ], was able to form fibrils in acid and high temperature conditions. Unlike the lysozyme, bovine insulin shows a negatively charged surface at neutral pH.…”

Precisely Defined Conjugated Oligoelectrolytes for Biosensing and Therapeutics

“…In addition to the oligothiophene-based COEs, oligo(p-phenylene ethynylene) derivatives (OPEs, structures see Figure 2) have also been reported as a novel molecular scaffold for detection of protein aggregates. [84][85] Similar to the LCOs, this class of molecules displayed a high selectivity for the aggregated form of the protein and OPEs were utilized to monitor the kinetics of amyloid fibril formation (Figure 3c-e). [84] From a library of compounds, molecular keys to the selective detection of the protein aggregates were identified (Figure 3f).…”