Inhibition potential evaluation of two synthetic bis-indole compounds on amyloid fibrillation: a molecular simulation study.

Protein aggregation is known as the main mechanism of amyloid fibrillation in amyloidosis diseases. Recent studies confirmed that compounds with one or two indole rings have inhibitory potential against amyloid fibrillation. Herein, the interaction of two similar compounds 'bis(indolyl)-2-methyl-phenyl-methene' and 'bis(indolyl)-2-chloro-phenyl-methene' with an amyloid core model was investigated. To this aim, molecular docking and all-atom molecular dynamics (MD) simulations were used. Docking results between aggregation-prone region (APR) of hen egg-white lysozyme (HEWL) and either of ligands showed that they interact with different residues of the APR (amyloid fibril nucleus). According to MD results, bis(indolyl)-2-methyl-phenyl-methene made a distance between the two cores, which was 1.5 times greater than that bis(indolyl)-2-chloro-phenyl-methene made. Analysis of RMSD/RMSF values revealed that bis(indolyl)-2-methyl-phenyl-methene stabilized strands of A and B, while destabilized strands C and D. The hydrophobic 'methyl' functional group in bis(indolyl)-2-methyl-phenyl-methene facilitate its deep penetration between core nuclei, via destabilizing outer strands of C and D. Considering this fact that results of this study are in agreement with experimental findings, details of the discovered mechanism of interaction between ligands and HEWL's APR would be inspiring for further anti-fibrillation drug designs.Communicated by Ramaswamy H. Sarma.

Colorimetric and label free detection of gelatinase positive bacteria and gelatinase activity based on aggregation and dissolution of gold nanoparticles.

A simple and sensitive method was developed for the detection of bacteria gelatinase activity based on their enzymatic hydrolysis effect on the surface plasmon resonance (SPR) of gelatin functionalized gold nanoparticles (Au@gelatin NPs) in bacteria supernatant. Characterization of synthesized NPs showed a very thin gelatin layer on the surface of about 20 nm AuNPs which modified the intrinsic SPR property of AuNPs. The extracted supernatants of applied bacteria were incubated with Au@gelatin NPs. Gelatinase activity of bacteria resulted in gradual gelatin shell removal and subsequent dissolution of bare AuNPs. The presence of inducer agents such as NaCl as the common ingredient in the bacterial medium led to the aggregation process of AuNPs and further bacterial activity resulted in AuNPs dissolution. AuNPs colloid solution color was changed from red to purple after addition of bacteria supernatants with gelatinase activity to the reaction. Also, the spectroscopic studies showed that the gelatinase activity of bacteria resulted in the gradual decrease of absorbance at 529 nm and subsequently led to extinction of SPR characteristics. So, the observed absorbance decrease in UV-Vis spectra at 529 nm was indicated as the gelatinase activity of applied bacteria. Different strains of gelatinase positive Bacillus strains were used as the real sample and their gelatinase activity was determined in the present study. Also, sensitivity analysis of the applied method was determined through this method and the obtained results showed Bacillus subtilis gelatinase activity in the linear range of 0-120 U/mL and detection limit of 0.5 U/mL. This method introduced label free, facile and sensitive assay of the bacterial gelatinase activity without any complicated instrument, affording convenience and simplicity.

Quantitative Measurement of the Affinity of Toxic and Nontoxic Misfolded Protein Oligomers for Lipid Bilayers and of its Modulation by Lipid Composition and Trodusquemine.

Many neurodegenerative diseases are associated with the self-assembly of peptides and proteins into fibrillar aggregates. Soluble misfolded oligomers formed during the aggregation process, or released by mature fibrils, play a relevant role in neurodegenerative processes through their interactions with neuronal membranes. However, the determinants of the cytotoxicity of these oligomers are still unclear. Here we used liposomes and toxic and nontoxic oligomers formed by the same protein to measure quantitatively the affinity of the two oligomeric species for lipid membranes. To this aim, we quantified the perturbation to the lipid membranes caused by the two oligomers by using the fluorescence quenching of two probes embedded in the polar and apolar regions of the lipid membranes and a well-defined protein-oligomer binding assay using fluorescently labeled oligomers to determine the Stern-Volmer and dissociation constants, respectively. With both approaches, we found that the toxic oligomers have a membrane affinity 20-25 times higher than that of nontoxic oligomers. Circular dichroism, intrinsic fluorescence, and FRET indicated that neither oligomer type changes its structure upon membrane interaction. Using liposomes enriched with trodusquemine, a potential small molecule drug known to penetrate lipid membranes and make them refractory to toxic oligomers, we found that the membrane affinity of the oligomers was remarkably lower. At protective concentrations of the small molecule, the binding of the oligomers to the lipid membranes was fully prevented. Furthermore, the affinity of the toxic oligomers for the lipid membranes was found to increase and slightly decrease with GM1 ganglioside and cholesterol content, respectively, indicating that physicochemical properties of lipid membranes modulate their affinity for misfolded oligomeric species.

Interaction, cytotoxicity and sustained release assessment of a novel anti-tumor agent using bovine serum albumin nanocarrier.

The interaction ability of bovine serum albumin (BSA) with 2,6-divanillylidenecyclohexanone (DVH) as a stable curcumin derivative was investigated using fluorescence and circular dichroism (CD) spectroscopy techniques under simulative physiological conditions (pH = 7.2). Following the obtained results of binding studies, bovine serum albumin nanoparticles (BSANPs) were synthesized and characterized using Fourier transform infrared spectroscopy (FT-IR), filed emission scanning electron microscopy (FE-SEM), atomic force microscope (AFM) and dynamic light scattering (DLS). The stable BSANPs showed a spherical shape with a diameter of 149.14 ± 46.69 nm and the formulation of BSA had no change during the fabrication process. DVH was loaded on BSANPs (DVH@BSANPs) and the release studies showed sustained release of DVH from BSANPs. The validation of DVH@BSANPs system confirmed that the Fickian release mechanism of DVH followed on Korsmeyer-Pepas model. The in vitro studies on HFFF2 and MDA-MB-231 were investigated using MTT assay, DAPI and annexinV/PI staining that showed biocompatible BSANPs reduced the cytotoxicity of DVH in normal cell lines significantly, and antitumor activity of DVH was increased when it was loaded onto BSANPs without necrosis. These results suggest that DVH@BSANPs are a novel biocompatible sustained release system for effective therapeutic approach.Communicated by Ramaswamy H. Sarma.

Identification of Novel 1,3,5-Triphenylbenzene Derivative Compounds as Inhibitors of Hen Lysozyme Amyloid Fibril Formation.

Deposition of soluble proteins as insoluble amyloid fibrils is associated with a number of pathological states. There is a growing interest in the identification of small molecules that can prevent proteins from undergoing amyloid fibril formation. In the present study, a series of small aromatic compounds with different substitutions of 1,3,5-triphenylbenzene have been synthesized and their possible effects on amyloid fibril formation by hen egg white lysozyme (HEWL), a model protein for amyloid formation, and of their resulting toxicity were examined. The inhibitory effect of the compounds against HEWL amyloid formation was analyzed using thioflavin T and Congo red binding assays, atomic force microscopy, Fourier-transform infrared spectroscopy, and cytotoxicity assays, such as the 3-(4,5-Dimethylthiazol)-2,5-Diphenyltetrazolium Bromide (MTT) reduction assay and caspase-3 activity measurements. We found that all compounds in our screen were efficient inhibitors of HEWL fibril formation and their associated toxicity. We showed that electron-withdrawing substituents such as -F and -NO2 potentiated the inhibitory potential of 1,3,5-triphenylbenzene, whereas electron-donating groups such as -OH, -OCH3, and -CH3 lowered it. These results may ultimately find applications in the development of potential inhibitors against amyloid fibril formation and its biologically adverse effects.

A genetic variant in CDKN2A/2B locus was associated with poor prognosis in patients with esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is among the leading causes of cancer related death. Despite of extensive efforts in identifying valid cancer prognostic biomarkers, only a very small number of markers have been identified. Several genetic variants in the 9p21 region have been identified that are associated with the risk of multiple cancers. Here, we explored the association of two genetic variants in the 9p21 region, CDKN2A/B, rs10811661, and rs1333049 for the first time in 273 subjects with, or without ESCC. We observed that the patients with ESCC had a higher frequency of a TT genotype for rs10811661 than individuals in the control group, and this polymorphism was also associated with tumor size. Moreover, a CC genotype for the rs1333049 polymorphism was associated with a reduced overall survival (OS) of patients with ESCC. In particular, patients with a CC (rs1333049) genotype had a significantly shorter OS (CC genotype: 34.5 ± 8.9 months vs. CG+GG: 47.7 ± 5.9 months; p value = 0.03). We have also shown the association of a novel genetic variant in CDKN2B gene with clinical outcome of patients with ESCC. Further investigations are warranted in a larger population to explore the value of emerging markers as a risk stratification marker in ESCC.

Bis(indolyl)phenylmethane derivatives are effective small molecules for inhibition of amyloid fibril formation by hen lysozyme.

Amyloid or similar protein aggregates are the hallmarks of many disorders, including Alzheimer's, Parkinson's, Huntington's diseases and amyloidoses. The inhibition of the formation of these aberrant species by small molecules is a promising strategy for disease treatment. However, at present, all such diseases lack an appropriate therapeutic approach based on small molecules. In this work we have evaluated five bis(indolyl)phenylmethane derivatives to reduce amyloid fibril formation by hen egg white lysozyme (HEWL) and its associated cytotoxicity. HEWL is a widely used model system to study the fundamentals of amyloid fibril formation and is heterologous to human lysozyme, which forms amyloid fibrils in a familial form of systemic amyloidosis. HEWL aggregation was tested in the presence and absence of the five compounds, under conditions in which the protein is partially unfolded. To this purpose, various techniques were used, including Congo red and Thioflavin T binding assays, atomic force microscopy, Fourier-Transform Infrared spectroscopy and cell-based cytotoxicity assays, such as the MTT reduction test and the trypan blue test. It was found that all compounds inhibited the formation of amyloid fibrils and their associated toxicity, diverging the aggregation process towards the formation of large, morphologically amorphous, unstructured, nontoxic aggregates, thus resembling class I molecules defined previously. In addition, the five compounds also appeared to disaggregate pre-formed fibrils of HEWL, which categorizes them into class IA. The half maximal inhibitory concentration (IC50) was found to be ca 12.3 ± 1.0 µM for the forefather compound.

Inhibition of amyloid fibril formation and cytotoxicity by a chemical analog of Curcumin as a stable inhibitor.

Clinical application of curcumin for Alzheimer's disease treatment is severely limited with regard to its poor bioavailability, high rate of metabolism, and instability under neutral condition. In the current study, we designed three compounds in which the diketone moiety of curcumin was replaced by cyclohexanone. In these compounds, the linker length of the molecules was optimal; and substitution of dioxolane for hydroxyl groups on compound 3 should prevent metabolic inactivation. The inhibitory effect of the compounds was investigated against hen egg white lysozyme (HEWL) fibrillation using AFM (atomic force microscope), ThT (thioflavin T) and MTT assay. We found that all three compounds were able to inhibit HEWL aggregation in a dose-dependent manner and inhibit the cytotoxic activity of aggregated HEWL. Docking results demonstrated that the compounds could bind into lysozyme and occupy the whole active site groove. In conclusion, we present chemical analogs of curcumin with various modifications in the spacer and the phenolic rings as improved inhibitors of amyloid aggregation.

Effect of Cinnamomum Verum Extract on the Amyloid Formation of Hen Egg-white Lysozyme and Study of its Possible Role in Alzheimer's Disease.

INTRODUCTION: Diagnosing and treating diseases associated with amyloid fibers remain a great challenge despite of intensive research carried out. One important approach in the development of therapeutics is the use of herbal extracts which are rich in aromatic small molecules. Cinnamomum verum extract (CE) contains proanthocyanidin and cinnamaldehyde, which have been suggested to be capable of directly inhibiting amyloid fibril formation in vitro. This study is aimed at characterizing the inhibitory activity of CE against the fibrillation of hen egg white lysozyme (HEWL). METHODS: Acidic pH and high temperatures were used to drive the protein towards amyloid formation. Lysozyme was dissolved at 2 mg/mL in 50mM glycine buffer (pH 2.5), and then incubated at 57 °C for the specified durations while stirred gently by Teflon magnetic bars. Various techniques including thioflavin T, fluorescence, Congo red absorbance assay and AFM micrography were used to characterize the HEWL fibrillation processes. RESULTS: In the absence of CE typical amyloid fibrils (like amyloids formed in Alzheimer disease) became evident after 48 h of incubation. Upon incubation with various extract concentrations in the range of 0.1-1 mg/ml, formation of fibrillar assemblies were significantly inhibited (P<0.05). AFM analysis and MTT assay also confirmed the role of the extract in amyloid inhibition. Our studies showed that the presence of CE did not have any effect on protein stabilization and thus directly interact with amyloid structure and inhibit formation of these structures. Furthermore, a docking experiment showed that a pi-pi interaction may occur between the aromatic component of cinnamaldehyde and W62. Interestingly, W62 is one of the principal aromatic residues that interact with glycine amide, which is an aggregation suppressor of HEWL. DISCUSSION: These observations suggest that aromatic small molecules of CE may directly insert into amyloidogenic core of early aggregates and inhibit amyloid fibril formation by disrupting the pi-pi interactions.

Oligomeric forms of insulin amyloid aggregation disrupt outgrowth and complexity of neuron-like PC12 cells.

Formation of protein amyloid fibrils consists of a series of intermediates including oligomeric aggregates, proto-fibrillar structures, and finally mature fibrils. Recent studies show higher toxicity for oligomeric and proto-fibrillar intermediates of protein relative to their mature fibrils. Here the kinetic of the insulin amyloid fibrillation was evaluated using a variety of techniques including ThT fluorescence, Congo red absorbance, circular dichroism, and atomic force microscopy (AFM). The solution surface tension changes were attributed to hydrophobic changes in insulin structure and were detected by Du Noüy Ring method. Determination of the surface tension of insulin oligomeric, proto-fibrillar and fibrillar forms indicated that the hydrophobicity of solution is enhanced by the formation of the oligomeric forms of insulin compared to other forms. In order to investigate the toxicity of the different forms of insulin we monitored morphological alterations of the differentiated neuron-like PC12 cells following incubation with native, oligomeric aggregates, proto-fibrillar, and fibrillar forms of insulin. The cell body area, average neurite length, neurite width, number of primary neurites, and percent of bipolar cells and node/primary neurite ratios were used to assess the growth and complexity of PC12 cells exposed to different forms of insulin. We observed that the oligomeric form of insulin impaired the growth and complexity of PC12 cells compared to other forms. Together our data suggest that the lower surface tension of oligomers and their perturbation affects the morphology of PC12 cells, mainly due to their enhanced hydrophobicity and detergent-like structures.

Thermal disaggregation of type B yeast hexokinase by indole derivatives: a mechanistic study.

Protein aggregation is a pathological hallmark of several human disorders, and a central problem in biotechnology, occurring during purification, sterilization, shipping and storage of protein structures. The process is a very complex one, characterized with a remarkable polymorphism of aggregates, including soluble amyloid oligomers, amyloid fibrils and amorphous species. While amyloid structure formation has been extensively investigated during the recent years, amorphous aggregation is still not well characterized. Use of small molecules that affect this process could be informative in this regard. In order to explore the inhibiting effect of small molecules on the amorphous aggregate formation, yeast hexokinase-B, a key enzyme in metabolism, has been chosen for the present study. Thermal aggregation of the enzyme was investigated in 50 mM phosphate buffer, pH 7 at 55°C and the extent of aggregation was measured by monitoring the increase in absorbance at 350 nm versus time. Possible anti-aggregation effects of a variety of non-specific ligands including indole, tryptophan, carbinol, and indomethacin were explored. Turbidity of the protein solutions was found to be diminished by the presence of these small molecules in the above conditions, with the highest effects being exerted by indomethacin. Dynamic light scattering and HPLC confirmed that indomethacin had the highest anti-aggregation effect. These observations, taken together, suggest that the indole ring is likely to play an important role in aggregation inhibition.

Large proteins have a great tendency to aggregate but a low propensity to form amyloid fibrils.

The assembly of soluble proteins into ordered fibrillar aggregates with cross-ß structure is an essential event of many human diseases. The polypeptides undergoing aggregation are generally small in size. To explore if the small size is a primary determinant for the formation of amyloids under pathological conditions we have created two databases of proteins, forming amyloid-related and non-amyloid deposits in human diseases, respectively. The size distributions of the two protein populations are well separated, with the systems forming non-amyloid deposits appearing significantly larger. We have then investigated the propensity of the 486-residue hexokinase-B from Saccharomyces cerevisiae (YHKB) to form amyloid-like fibrils in vitro. This size is intermediate between the size distributions of amyloid and non-amyloid forming proteins. Aggregation was induced under conditions known to be most effective for amyloid formation by normally globular proteins: (i) low pH with salts, (ii) pH 5.5 with trifluoroethanol. In both situations YHKB aggregated very rapidly into species with significant ß-sheet structure, as detected using circular dichroism and X-ray diffraction, but a weak Thioflavin T and Congo red binding. Moreover, atomic force microscopy indicated a morphology distinct from typical amyloid fibrils. Both types of aggregates were cytotoxic to human neuroblastoma cells, as indicated by the MTT assay. This analysis indicates that large proteins have a high tendency to form toxic aggregates, but low propensity to form regular amyloid in vivo and that such a behavior is intrinsically determined by the size of the protein, as suggested by the in vitro analysis of our sample protein.

Thermally induced changes in the structure and activity of yeast hexokinase B.

Yeast hexokinase has been poorly characterized in regard with its stability. In the present study, various spectroscopic techniques were employed to investigate thermal stability of the monomeric form of yeast hexokinase B (YHB). The enzyme underwent a conformational transition with a T(m) of about 41.9 degrees C. The structural transition proved to be significantly reversible below 55 degrees C and irreversible at higher temperatures. Thermoinactivation studies revealed that enzymatic activity diminished significantly at high temperatures, with greater loss of activity observed above 55 degrees C. Release of ammonia upon deamidation of YHB obeyed a similar temperature-dependence pattern. Dynamic light scattering and size exclusion-HPLC indicated formation of stable aggregates. Taking various findings on the influence of osmolytes and chaperone-like agents on YHB thermal denaturation together, it is proposed that the purely conformational transition of YHB is reversible, and irreversibility is due to aggregation, as a major cause. Deamidation of a critical Asn or Gln residue(s) may also play an important role.

Thermal aggregation of alpha-chymotrypsin: role of hydrophobic and electrostatic interactions.

We have recently reported that electrostatic interactions may play a critical role in alcohol-induced aggregation of alpha-chymotrypsin (CT). In the present study, we have investigated the heat-induced aggregation of this protein. Thermal aggregation of CT obeyed a characteristic pattern, with a clear lag phase followed by a sharp rise in turbidity. Intrinsic and ANS fluorescence studies, together with fluorescence quenching by acrylamide, suggested that the hydrophobic patches are more exposed in the denatured conformation. Typical chaperone-like proteins, including alpha- and beta-caseins and alpha-crystalline could inhibit thermal aggregation of CT, and their inhibitory effect was nearly pH-independent (within the pH range of 7-9). This was partially counteracted by alpha-, beta- and especially gamma-cyclodextrins, suggesting that hydrophobic interactions may play a major role. Loss of thermal aggregation at extreme acidic and basic conditions, combined with changes in net charge/pH profile of aggregation upon chemical modification of lysine residues are taken to support concomitant involvement of electrostatic interactions.

A study on the two binding sites of hexokinase on brain mitochondria.

BACKGROUND: Type I hexokinase (HK-I) constitutes the predominant form of the enzyme in the brain, a major portion of which is associated with the outer mitochondrial membrane involving two sets of binding sites. In addition to the glucose-6-phosphate (G6P)-sensitive site (Type A), the enzyme is bound on a second set of sites (Type B) which are, while insensitive to G6P, totally releasable by use of high concentrations of chaotropic salts such as KSCN. Results obtained on release of HK-I from these "sites" suggested the possibility for the existence of distinct populations of the bound enzyme, differing in susceptibility to release by G6P. RESULTS: In the present study, the sensitivity of HK-I toward release by G6P (2 mM) and a low concentration of KSCN (45 mM) was investigated using rat brain, bovine brain and human brain mitochondria. Partial release from the G6P-insensitive site occurred without disruption of the mitochondrial membrane as a whole and as related to HK-I binding to the G6P-sensitive site. While, as expected, the sequential regime release-rebinding-release was observed on site A, no rebinding was detectable on site B, pre-treated with 45 mM KSCN. Also, no binding was detectable on mitochondria upon blocking site A for HK-I binding utilizing dicyclohexylcarbodiimide (DCCD), followed by subsequent treatment with KSCN. These observations while confirmed the previously-published results on the overall properties of the two sites, demonstrated for the first time that the reversible association of the enzyme on mitochondria is uniquely related to the Type A site. CONCLUSION: Use of very low concentrations of KSCN at about 10% of the level previously reported to cause total release of HK-I from the G6P- insensitive site, caused partial release from this site in a reproducible manner. In contrast to site A, no rebinding of the enzyme takes place on site B, suggesting that site A is 'the only physiologically-important site in relation to the release-rebinding of the enzyme which occur in response to the energy requirements of the brain. Based on the results presented, a possible physiological role for distribution of the enzyme between the two sites on the mitochondrion is proposed.