Many amyloid inhibitors resemble molecules that form chemical aggregates which are known to inhibit many proteins. conformation1. Though there are no approved therapies targeting amyloid formation directly many organic molecules inhibit fibrillization in vitro2-7. Some such as the chelator clioquinol (1) even have activity in vivo4. These results have inspired the hope of therapeutic applications for some molecules3-5. Curiously many fibrillization inhibitors resemble molecules known to form promiscuous chemical aggregates. These colloidal particles are composed of small organic molecules Fosamprenavir and range in size from 50 to over 600 nm8. Once formed they actually sequester proteins and inhibit enzymes nonspecifically8 9 Like many inhibitors of amyloid polymerization these colloidal inhibitors are typically highly conjugated hydrophobic and dye-like (Supplementary Table 1 online)8 9 A good example is the amyloid inhibitor Congo red (2) a dye that was one of the first molecules observed to exhibit colloidal inhibition8. The flavonoid baicalein (3) an inhibitor of α-synuclein polymerization6 resembles the known chemical aggregator quercetin (4) and 4 5 (DAPH 5 an inhibitor of Alzheimer’s amyloid formation2 resembles the aggregator bisindoylmaleimide (6; Supplementary Fig. 1 online). Given that chemical aggregates function through enzyme sequestration we wondered whether they might also sequester protein molecules from each other thereby preventing amyloid polymerization. Here we investigate this hypothesis in two classic amyloid-forming proteins: the yeast prion protein Sup35 (ref. 10) and the recombinant mouse prion protein recMoPrP89-230 (ref. 11). We inquire whether known chemical aggregators can inhibit amyloid fiber formation whether known fibrillization inhibitors form colloidal aggregates and whether amyloid inhibition by these molecules is in fact mediated via colloidal aggregation. Eight known chemical aggregators and two known nonaggregators8 9 were tested for inhibition of Sup35 fibrillization in a thioflavin T (ThT 7 fluorescence assay. All eight inhibited Sup35 fibrillization both in seeded and unseeded polymerization reactions whereas the two nonaggregators were Fosamprenavir inactive (Table 1 and Supplementary Fig. 2a b online). Likewise three amyloid inhibitors (DAPH baicalein and clioquinol) also inhibited Sup35 polymerization. Among the most potent molecules was the chemical aggregator tetraiodophenolphthalein (TIPT 8 which had a half-maximal inhibitory Fosamprenavir concentration (IC50) of 2.5 μM (Fig. 1a). To control for spectroscopic interference we also tested two chemical aggregate-forming molecules for inhibition by dynamic light scattering (DLS). At 2 μM TIPT the DLS reaction was 30% inhibited and at 20 μM the reaction was more than 99% inhibited. Similarly the reaction with 25 μM of clotrimazole (9) was 98% inhibited (Supplementary Fig. 2c d). Figure 1 Chemical aggregators inhibit amyloid formation in biochemical assays. (a) The known chemical aggregators TIPT and clotrimazole inhibit seeded Sup35 polymerization in a dose-dependent manner. Inhibition of Sup35 polymerization was measured by ThT fluorescence … Table 1 Inhibition of amyloid polymerization Given that aggregate-based inhibition is nonspecific chemical aggregators KT3 Tag antibody should also inhibit other amyloidogenic proteins. In a ThT-based assay six of the eight colloidal inhibitors also inhibited fibrillization of the mouse prion protein (recMoPrP). In most cases potency was lower than that observed against Sup35 (Table 1) which is likely due to the use of 3 M urea in the recMoPrP assay a condition that is known to disrupt the formation of colloidal aggregates8. Consistent with this view one of the chemical aggregators that did not inhibit recMoPrP fiber formation TIPT did do so in an electron microscopy assay that lacked urea. TIPT particles not only associated with preformed recMoPrP fibers but also inhibited fibrillization resulting in a grid empty of fibers (Supplementary Fig. 3 online). If known chemical aggregators inhibit fibrillization do known fibrillization inhibitors form colloidal aggregates? We tested five published amyloid inhibitors for detergent-sensitive inhibition of β-lactamase (Supplementary Table 2 online)..