Amyloid Fibrils Research Articles

Molecular mechanism of alpha- and beta-cyclodextrin assisted refolding of SDS-induced amyloid fibrils of myoglobin

The formation of amyloids arises from the misfolding or unfolding of various proteins. This study investigated the impact of chemical chaperones, alpha-cyclodextrin (α-CD) and beta-cyclodextrin (β-CD), on the solubilization and defibrillation of sodium dodecyl sulfate (SDS)-induced myoglobin (Mb) amyloid fibrils. Amyloid fibril was developed in Mb in the presence of 0.8 mmol dm−3 SDS at pH 4.5. Subsequently, SDS-induced Mb amyloid was incubated with varying concentrations of α-CD and β-CD at the same pH. Our turbidity, intrinsic fluorescence, SDS-PAGE, and transmission electron microscope data showed that α-CD (2.1 mmol dm−3) was more efficiently solubilized the SDS-treated Mb aggregates than β-CD (4.0 mmol dm−3). But, another interesting phenomenon was observed with β-CD. The ThT fluorescence and far-UV CD data suggested that amyloid defibrillation by β-CD (0.6 mmol dm−3) was more effective than α-CD (0.9 mmol dm−3). The intrinsic fluorescence and far-UV CD data also showed that SDS-treated Mb regained native-like structure at lower α-CD compared to β-CD. Overall our data suggest that α-CD was more efficient in aggregate solubilization while β-CD was more effective in amyloid defibrillation. Understanding the mechanisms underlying cyclodextrins’ actions may serve as a basis for identifying potential drugs to suppress amyloid fibril formation effectively. This research provides valuable insights into mitigating amyloid-related pathologies.

Unraveling the hydration dynamics of ACC1–13K24 with ATP: From liquid to droplet to amyloid fibril

In order to achieve a comprehensive understanding of protein aggregation processes, an exploration of solvation dynamics, a key yet intricate component of biological phenomena, is mandatory. In the present study, we used Fourier transform infrared spectroscopy and terahertz spectroscopy complemented by atomic force microscopy and kinetic experiments utilizing thioflavin T fluorescence to elucidate the changes in solvation dynamics during liquid-liquid phase separation and subsequent amyloid fibril formation, the latter representing a transition from liquid to solid phase separation. These processes are pivotal in the pathology of neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. We focus on the ACC1–13K24-ATP protein complex, which undergoes fibril formation followed by droplet generation. Our investigation reveals the importance of hydration as a driving force in these processes, offering new insights into the molecular mechanisms at play.

β‐lactoglobulin amyloid fibrils and their binding properties towards uranyl‐ions

β‐lactoglobulin amyloid fibrils and their binding properties towards uranyl‐ions

Capturing the illusive ring-shaped intermediates in Aβ42 amyloid formation.

Protein/peptide amyloid fibril formation is associated with various neurodegenerative diseases and, hence, has been the subject of extensive studies. From a structure-evolution point of view, we now know a great deal about the initial and final states of this process; however, we know very little about its intermediate states. Herein, we employ liquid-phase transmission electron microscopy to directly visualize the formation of one of the intermediates formed during the aggregation process of an amyloid-forming peptide. As shown in figure, we find that Aβ42, the amyloid formation of which has been linked to the development of Alzheimer's disease, can populate a ring-shaped intermediate structure with a diameter of tens of nanometers; additionally, the air-liquid interface can "catalyze" the formation of amyloid fibrils.

Morphological and Biophysical Study of S100A9 Protein Fibrils by Atomic Force Microscopy Imaging and Nanomechanical Analysis.

Atomic force microscopy (AFM) imaging enables the visualization of protein molecules with high resolution, providing insights into their shape, size, and surface topography. Here, we use AFM to study the aggregation process of protein S100A9 in physiological conditions, in the presence of calcium at a molar ratio 4Ca2+:S100A9. We find that S100A9 readily assembles into a worm-like fibril, with a period dimension along the fibril axis of 11.5 nm. The fibril's chain length extends up to 136 periods after an incubation time of 144 h. At room temperature, the fibril's bending stiffness was found to be 2.95×10-28 Nm2, indicating that the fibrils are relatively flexible. Additionally, the values obtained for the Young's modulus (Ex=6.96×105 Pa and Ey=3.37×105 Pa) are four orders of magnitude lower than those typically reported for canonical amyloid fibrils. Our findings suggest that, under the investigated conditions, a distinct aggregation mechanism may be in place in the presence of calcium. Therefore, the findings reported here could have implications for the field of biomedicine, particularly with regard to Alzheimer's disease.

Hydrogen bonding patterns and cooperativity in polyproline II helical bundles

Hydrogen bond cooperativity (HBC) plays an important role in stabilizing protein assemblies built by α-helices and β-sheets, the most common secondary structures. However, whether HBC exists in other types of protein secondary structures such as polyproline II (PPII) helices remains unexplored. This is intriguing, since PPII systems as assembling blocks are continuously emerging across multiple fields. Here, using a combination of computational chemistry tools and molecular modeling corroborated by experimental observables, we characterize the distinct H-bonding patterns present in PPII helical bundles and establish that HBC stabilizes intermolecular PPII helices as seen in other protein assemblies such as amyloid fibrils. In addition to cooperative interactions in canonical CO···HN H-bonds, we show that analogous interactions in non-canonical CO···HαCα H-bonds are relevant in Gly-rich PPII bundles, thus compensating for the inability of glycine residues to create hydrophobic cores. Our results provide a mechanistic explanation for the assembly of these bundles.

Amylum forms typical self-assembled amyloid fibrils.

Amyloid fibril formation is a central biochemical process in pathology and physiology. Over decades, substantial advances were made in elucidating the mechanisms of amyloidogenesis, its links to disease, and the production of functional supramolecular structures. While the term "amyloid" denotes starch-like features of these assemblies, no evidence of amyloidogenic behavior of polysaccharides has been so far reported. Here, we investigate the potential of amylum (starch) not only to self-assemble into hierarchical fibrillar structures but also to exhibit canonical amyloidogenic properties. Ordered amylum structures were formed through a sigmoidal growth process with characteristic amyloid features including typical nanofibril morphology, binding to indicative dyes, inherent luminescence, apple-green birefringence upon Congo red staining, and notable mechanical rigidity. These findings shed light on polysaccharide self-assembly and expand the generic amyloid phenomenon.

Inhibition of amyloid beta oligomer, fibrils, and peptide using nanoparticles to disrupt Alzheimer's pathogenesis.

The Aβ peptide, which is connected to the development of Alzheimer's disease, forms highly neurotoxic prefibrillar oligomeric aggregates, which are challenging to study due to their fleeting, low prevalence, and diverse nature. These aggregates are considered to play a role in the pathogenesis of numerous neurodegenerative diseases. The potential approach of blocking or disrupting the buildup of amyloid peptides, particularly amyloid-β (AβOs), by using nanoparticles that specifically bind or prevent their aggregation to develop new medications and treatments for Alzheimer's disease (AD) could be a promising solution. Nanoparticles have been proposed as a potential solution to modify the protein fibrillation process. Recently, Researchers have design and created some nanoparticles for inhibition of amyloid-β oligomer and (Aβ) peptide aggregation, involved in Alzheimer’s disease (AD). In this concise review, we concentrated on the mechanism and formation of amyloid beta oligomers, fibrils, peptides, and it’s role in Alzheimer's disease. Secondly, we discussed small molecules that can detect various forms of amyloid beta for early diagnosis. Lastly, we primarily focused on nanoparticles that possess the ability to inhibit and disaggregate amyloid beta oligomers fibrils, and peptide which are the primary hallmarks of Alzheimer's disease. Here for the first time we also summarize some of the nanoparticles and nanomaterials which can dis-aggregate the exis-ting amyloid-β oligomer and (Aβ) peptide which are challenging for many researcher.

Simulating the anti-aggregative effect of fasudil in early dimerisation process of α-synuclein

The aggregation of the protein α-synuclein into amyloid deposits is associated with multiple neurological disorders, including Parkinson's disease. Soluble amyloid oligomers are reported to exhibit higher toxicity than insoluble amyloid fibrils, with dimers being the smallest toxic oligomer. Small molecule drugs, such as fasudil, have shown potential in targeting α-synuclein aggregation and reducing its toxicity. In this study, we use atomistic molecular dynamics simulations to demonstrate how fasudil affects the earliest stage of aggregation, namely dimerization. Our results show that the presence of fasudil reduces the propensity for intermolecular contact formation between protein chains. Consistent with previous reports, our analysis confirms that fasudil predominantly interacts with the negatively charged C-terminal region of α-synuclein. However, we also observe transient interactions with residues in the charged N-terminal and hydrophobic NAC regions. Our simulations indicate that while fasudil prominently interacts with the C-terminal region, it is the transient interactions with residues in the N-terminal and NAC regions that effectively block the formation of intermolecular contacts between protein chains and prevent early dimerization of this disordered protein.

Selective detection of alpha synuclein amyloid fibrils by faradaic and non-faradaic electrochemical impedance spectroscopic approaches

This study utilized faradaic and non-faradaic electrochemical impedance spectroscopy to detect alpha synuclein amyloid fibrils on gold interdigitated tetraelectrodes (AuIDTE), providing valuable insights into electrochemical reactions for clinical use. AuIDE was purchased, modified with zinc oxide for increased hydrophobicity. Functionalization was conducted with hexacyanidoferrate and carbonyldiimidazole. Faradaic electrochemical impedance spectroscopy has been extensively explored in clinical diagnostics and biomedical research, providing information on the performance and stability of electrochemical biosensors. This understanding can help develop more sensitive, selective, and reliable biosensing platforms for the detection of clinically relevant analytes like biomarkers, proteins, and nucleic acids. Non-faradaic electrochemical impedance spectroscopy measures the interfacial capacitance at the electrode–electrolyte interface, eliminating the need for redox-active species and simplifying experimental setups. It has practical implications in clinical settings, like real-time detection and monitoring of biomolecules and biomarkers by tracking changes in interfacial capacitance. The limit of detection (LOD) for normal alpha synuclein in faradaic mode is 2.39-fM, The LOD for aggregated alpha synuclein detection is 1.82-fM. The LOD for non-faradaic detection of normal alpha synuclein is 2.22-fM, and the LOD for nonfaradaic detection of aggregated alpha synuclein is 2.40-fM. The proposed EIS-based AuIDTEs sensor detects alpha synuclein amyloid fibrils and it is highly sensitive.

Piperonal protects neuron-like and retinalpigment epithelial (RPE) cells from oxidative stress and apoptosis through inhibition of α-synuclein aggregation

Protein fibrillation is a crucial process in the onset of several neurodegenerative and retinal disorders due to the formation of cytotoxic species. Because of their capacity to prevent protein aggregation, small molecules have the potential to be appointed as therapeutic agents. Here, we examined the inhibitory impacts of the piperonal as a carbaldehyde-derived compound on the fibrillation process of α-synuclein and underlying cytotoxicity against neuron-like (PC12) and human retinal pigment epithelial (RPE) (ARPE-19) cells. The results showed that the values of kapp and lag time of α-synuclein were modulated with piperonal. Moreover, ANS fluorescence intensity analysis indicated that piperonal can inhibit the formation of a molten global (misfolded) state of α-synuclein, which is a necessary step in the formation of protein amyloid fibrils. Congo red absorption and circular dichroism spectroscopy also verified the inhibition of β-sheet structure formation after treatment of α-synuclein with piperonal. Furthermore, theoretical studies displayed that piperonal interacts with VAL40:HN, GLU35:O, VAL40, and LYS43 amino acid residues and forms a complex. In addition, cytotoxicity assays demonstrated that piperonal as a safe small molecule could mitigate the induced cytotoxicity by α-synuclein amyloids in PC12 and ARPE-19 cells through reduction of ROS and Bax/Bcl2 mRNA overexpression. Taken together, these outcomes showed that piperonal as a natural aldehyde compound can inhibit α-synuclein fibrillation and underlying cytotoxicity which may be developed for potential therapeutic applications in vivo.

Epidemiological Changes in Transthyretin Cardiac Amyloidosis: Evidence from In Vivo Data and Autoptic Series.

Cardiac amyloidosis is an infiltrative disease that causes progressive myocardial impairment secondary to amyloid fibril deposition in the extracellular space of the myocardium. Many amyloid precursors, including transthyretin protein, are known to determine cardiac damage by aggregating and precipitating in cardiac tissue. Transthyretin cardiac amyloidosis may be either caused by rare genetic mutations of the transthyretin gene in the hereditary variant, or may arise as a consequence of age-related mechanisms in the acquired form. Although it has been labeled as a rare disease, in recent years, transthyretin cardiac amyloidosis has stood out as an emerging cause of aortic stenosis, unexplained left ventricular hypertrophy and heart failure with preserved ejection fraction, particularly in the elderly. Indeed, the integration of data deriving from both in vivo imaging techniques (whose advancement in the last years has allowed to achieve an easier and more accessible non-invasive diagnosis) and forensic studies (showing a prevalence of amyloid deposition in cardiac tissue of elderly patients up to 29%) suggests that cardiac amyloidosis is a more common disease than traditionally considered. Thanks to all the improvements in non-invasive diagnostic techniques, along with the development of efficacious therapies offering improvements in survival rates, transthyretin cardiac amyloidosis has been transformed from an incurable and infrequent condition to a relatively more diffuse and treatable disease, which physicians should take into consideration in the differential diagnostic processes in daily clinical practice.

Modification of rice protein and its components: Enhanced fibrils formation and improved foaming properties

Plant-derived proteins like rice protein are considered an ideal source for yielding amyloid fibrils due to sustainability and affordability. However, the inherent low solubility of rice protein often restricts its self-assembly capability under common fibrillization protocols. Hence, this study comprehensively investigated the effect of modification on the self-assembly behavior, protein structure and foaming properties of rice protein and its components. The modification facilitated the transformation of α-helix to β-sheet, promoting fibrils formation. All modified proteins, except rice protein, exhibited significantly increased zeta potential values. AFM results revealed that the modified rice protein and globulin fibrils exhibited entangled aggregation behavior, while the glutelin fibril was notably extended, with several micrometers in length. Additionally, modification promoted the aggregation of albumin and prolamin particles to form short and straight fibrils. Amino acid analysis indicated that the content difference of amino acids with different characteristics and the change of aromatic amino acid interaction caused by modification may lead to different self-assembly behavior of the same protein. Furthermore, the foaming capability and stability of most protein fibrils were significantly improved by the modification. These findings provide valuable insights into the regulation of plant-derived protein fibrillation through modification.

On the pH-dependence of α-synuclein amyloid polymorphism and the role of secondary nucleation in seed-based amyloid propagation

The aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the α-synuclein fibrils hampers efforts in disease-relevant in vitro studies on α-synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of α-synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8–7.4, a pH-dependent selection between Type 1, 2, and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.

On the pH-dependence of α-synuclein amyloid polymorphism and the role of secondary nucleation in seed-based amyloid propagation.

The aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the α-synuclein fibrils hampers efforts in disease-relevant in vitro studies on α-synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of α-synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8-7.4, a pH-dependent selection between Type 1, 2, and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.

Islet amyloid polypeptide fibril catalyzes amyloid-β aggregation by promoting fibril nucleation rather than direct axial growth

Aberrant aggregation of amyloid-β (Aβ) and islet amyloid polypeptide (IAPP) into amyloid fibrils underlies the pathogenesis of Alzheimer's disease (AD) and type 2 diabetes (T2D), respectively. T2D significantly increases AD risk, with evidence suggesting that IAPP and Aβ co-aggregation and cross-seeding might contribute to the cross-talk between two diseases. Experimentally, preformed IAPP fibril seeds can accelerate Aβ aggregation, though the cross-seeding mechanism remains elusive. Here, we computationally demonstrated that Aβ monomer preferred to bind to the elongation ends of preformed IAPP fibrils. However, due to sequence mismatch, the Aβ monomer could not directly grow onto IAPP fibrils by forming multiple stable β-sheets with the exposed IAPP peptides. Conversely, in our control simulations of self-seeding, the Aβ monomer could axially grow on the Aβ fibril, forming parallel in-register β-sheets. Additionally, we showed that the IAPP fibril could catalyze Aβ fibril nucleation by promoting the formation of parallel in-register β-sheets in the C-terminus between bound Aβ peptides. This study enhances our understanding of the molecular interplay between Aβ and IAPP, shedding light on the cross-seeding mechanisms potentially linking T2D and AD. Our findings also underscore the importance of clearing IAPP deposits in T2D patients to mitigate AD risk.

Quantum-enhanced photoprotection in neuroprotein architectures emerges from collective light-matter interactions

BackgroundSuperradiance is the phenomenon of many identical quantum systems absorbing and/or emitting photons collectively at a higher rate than any one system can individually. This phenomenon has been studied analytically in idealized distributions of electronic two-level systems (TLSs), each with a ground and excited state, as well as numerically in realistic photosynthetic nanotubes and cytoskeletal architectures.MethodsSuperradiant effects are studied here in idealized toy model systems and realistic biological mega-networks of tryptophan (Trp) molecules, which are strongly fluorescent amino acids found in many proteins. Each Trp molecule acts as a chromophore absorbing in the ultraviolet spectrum and can be treated approximately as a TLS, with its 1La excited singlet state; thus, organized Trp networks can exhibit superradiance. Such networks are found, for example, in microtubules, actin filaments, and amyloid fibrils. Microtubules and actin filaments are spiral-cylindrical protein polymers that play significant biological roles as primary constituents of the eukaryotic cytoskeleton, while amyloid fibrils have been targeted in a variety of neurodegenerative diseases. We treat these proteinaceous Trp networks as open quantum systems, using a non-Hermitian Hamiltonian to describe interactions of the chromophore network with the electromagnetic field. We numerically diagonalize the Hamiltonian to obtain its complex eigenvalues, where the real part is the energy and the imaginary part is its associated enhancement rate. We also consider multiple realizations of increasing static disorder in either the site energies or the decay rates.ResultsWe obtained the energies and enhancement rates for realistic microtubules, actin filament bundles, and amyloid fibrils of differing lengths, and we use these values to calculate the quantum yield, which is the ratio of the number of photons emitted to the number of photons absorbed. We find that all three of these structures exhibit highly superradiant states near the low-energy portion of the spectrum, which enhances the magnitude and robustness of the quantum yield to static disorder and thermal noise.ConclusionThe high quantum yield and stable superradiant states in these biological architectures may play a photoprotective role in vivo, downconverting energetic ultraviolet photons—absorbed from those emitted by reactive free radical species—to longer, safer wavelengths and thereby mitigating biochemical stress and photophysical damage. Contrary to conventional assumptions that quantum effects cannot survive in large biosystems at high temperatures, our results suggest that macropolymeric collectives of TLSs in microtubules, actin filaments, and amyloid fibrils exhibit increasingly observable and robust effects with increasing length, up to the micron scale, due to quantum coherent interactions in the single-photon limit. Superradiant enhancement and high quantum yield exhibited in neuroprotein polymers could thus play a crucial role in information processing in the brain, the development of neurodegenerative diseases such as Alzheimer’s and related dementias, and a wide array of other pathologies characterized by anomalous protein aggregates.

HSP110 is a modulator of amyloid beta (Aβ) aggregation and proteotoxicity.

Chaperones safeguard protein homeostasis by promoting folding and preventing aggregation. HSP110 is a cytosolic chaperone that functions as a nucleotide exchange factor for the HSP70 cycle. Together with HSP70 and a J-domain protein (JDP), HSP110 maintains protein folding and resolubilizes aggregates. Interestingly, HSP110 is vital for the HSP70/110/JDP-mediated disaggregation of amyloidogenic proteins implicated in neurodegenerative diseases (i.e., α-synuclein, HTT, and tau). However, despite its abundance, HSP110 remains still an enigmatic chaperone, and its functional spectrum is not very well understood. Of note, the disaggregation activity of neurodegenerative disease-associated amyloid fibrils showed both beneficial and detrimental outcomes invivo. To gain a more comprehensive understanding of the chaperone HSP110 invivo, we analyzed its role in neuronal proteostasis and neurodegeneration in C. elegans. Specifically, we investigated the role of HSP110 in the regulation of amyloid beta peptide (Aβ) aggregation using an established Aβ-C. elegans model that mimics Alzheimer's disease pathology. We generated a novel C. elegans model that over-expresses hsp-110pan-neuronally, and we also depleted hsp-110 by RNAi-mediated knockdown. We assessed Aβ aggregation invivo and insitu by fluorescence lifetime imaging. We found that hsp-110 over-expression exacerbated Aβ aggregation and appeared to reduce the conformational variability of the Aβ aggregates, whereas hsp-110 depletion reduced aggregation more significantly in the IL2 neurons, which marked the onset of Aβ aggregation. HSP-110 also plays a central role in growth and fertility as its over-expression compromises nematode physiology. In addition, we found that HSP-110 modulation affects the autophagy pathway. While hsp-110 over-expression impairs the autophagic flux, a depletion enhances it. Thus, HSP-110 regulates multiple nodes of the proteostasis network to control amyloid protein aggregation, disaggregation, and autophagic clearance.

Concentration effect of zinc ions on amyloid fibrillation of hen egg-white lysozyme with thermal treatment revealed by Raman spectroscopy

Accumulation of Zn2+ ions in protein aggregates has been suggested to be a key factor in Alzheimer’s disease etiology. However, the specific influence of Zn2+ ions on the formation of amyloid fibrils or amorphous aggregates is still much debated. Herein, we conducted a combined study of Raman spectroscopy, UV–vis absorption spectroscopy and ThT fluorescence assay on the concentration effects of Zn2+ ions on amyloid fibrillation of hen egg-white lysozyme with thermal treatment. The addition of Zn2+ ions showed a negligible effect on unfolding of the protein tertiary structures and nucleation pathways on amyloid fibrillation. In contrast, a distinct concentration-dependence was observed for the influence of Zn2+ ions on the transformation of lysozyme secondary structures. At low concentration, the metal ions do not affect the populations of major secondary structures in the final state after incubation, while they at high concentration exhibit a promotion effect on the transformation from α-helix to β-sheet-like structures. These findings provide insights into the multifaceted impact of Zn2+ ions on protein aggregation, shedding light on potential therapeutic strategies for neurodegenerative diseases.

Binding adaptability of chemical ligands to polymorphic α-synuclein amyloid fibrils

α-synuclein (α-syn) assembles into structurally distinct fibril polymorphs seen in different synucleinopathies, such as Parkinson's disease and multiple system atrophy. Targeting these unique fibril structures using chemical ligands holds diagnostic significance for different disease subtypes. However, the molecular mechanisms governing small molecules interacting with different fibril polymorphs remain unclear. Here, we investigated the interactions of small molecules belonging to four distinct scaffolds, with different α-syn fibril polymorphs. Using cryo-electron microscopy, we determined the structures of these molecules when bound to the fibrils formed by E46K mutant α-syn and compared them to those bound with wild-type α-syn fibrils. Notably, we observed that these ligands exhibit remarkable binding adaptability, as they engage distinct binding sites across different fibril polymorphs. While the molecular scaffold primarily steered the binding locations and geometries on specific sites, the conjugated functional groups further refined this adaptable binding by fine-tuning the geometries and binding sites. Overall, our finding elucidates the adaptability of small molecules binding to different fibril structures, which sheds light on the diagnostic tracer and drug developments tailored to specific pathological fibril polymorphs.