Atomic Insight on Inhibition of Fibrillization of Dipeptides by Replacement of Phenylalanine with Tryptophan.

Tryptophan (Trp) conjugates destabilize amyloid fibrils responsible for amyloidoses. However, the mechanism of such destabilization is obscure. Herein the self-assembly of four synthesized Trp-containing dipeptides Boc-xxx-Trp-OMe (xxx: Val, Leu, Ile, and Phe) has been investigated and compared with the existing report on their Phe congeners. Two among them are the C-terminal tryptophan analogs of Boc-Val-Phe-OMe (VF, Aß18-19) and Boc-Phe-Phe-OMe (FF, Aß19-20), part of the central hydrophobic region of amyloid-ß (Aß1-42). While Boc-Val-Trp-OMe (VW), Boc-Leu-Trp-OMe (LW), Boc-Ile-Trp-OMe (IW), and Boc-Phe-Trp-OMe (FW) displayed a spherical morphology in FESEM and AFM images, the corresponding phenylalanine-containing dipeptides displayed various fibrous structures. Single-crystal X-ray diffraction (SC-XRD) indicated that peptides VW and IW exhibited structures containing parallel ß-sheet, cross-ß-structure, sheet-like layer structure, and helical arrangement in the solid state. Interestingly, peptide FW displayed inverse γ-turn conformation (similar to open-turn structure), antiparallel ß-sheet structure, columnar structure, supramolecular nanozipper structure, sheet-like layer arrangement, and helical architecture in the solid state. The open-turn conformation and nanozipper structure formation by FW may be the first example of a dipeptide that forms such structures. The minute but consistent differences in molecular packing at the atomic level between Trp and Phe congeners may be responsible for their remarkably different supramolecular structure generation. This molecular-level structural analysis may be helpful for the de novo design of peptide nanostructures and therapeutics. Similar studies by the Debasish Haldar group are reported, but they investigated the inhibition of fibrillization of dipeptides by tyrosine and interactions are expectedly different.

Functional Characterization of the Odorant Receptor 51E2 in Human Melanocytes.

Olfactory receptors, which belong to the family of G-protein-coupled receptors, are found to be ectopically expressed in non-sensory tissues mediating a variety of cellular functions. In this study we detected the olfactory receptor OR51E2 at the transcript and the protein level in human epidermal melanocytes. Stimulation of primary melanocytes with the OR51E2 ligand ß-ionone significantly inhibited melanocyte proliferation. Our results further showed that ß-ionone stimulates melanogenesis and dendritogenesis. Using RNA silencing and receptor antagonists, we demonstrated that OR51E2 activation elevated cytosolic Ca(2+) and cAMP, which could mediate the observed increase in melanin synthesis. Co-immunocytochemical stainings using a specific OR51E2 antibody revealed subcellular localization of the receptor in early endosomes associated with EEA-1 (early endosome antigen 1). Plasma membrane preparations showed that OR51E2 protein is present at the melanocyte cell surface. Our findings thus suggest that activation of olfactory receptor signaling by external compounds can influence melanocyte homeostasis.

Dynamic combinatorial enrichment of polyconformational D-/L-peptide dimers.

D-/L-peptides such as gramicidin A (gA) adopt unique dimeric ß-helical structures of different topologies. To overcome their conformational promiscuity and enrich individual components, a dynamic combinatorial approach assisted by thiol tags was developed. This method led to identification of the preferential formation of antiparallel dimers under a broad range of conditions, which was independent of peptide side-chain polarity. Exclusive formation of an antiparallel cyclic dimer was achieved in the presence of cesium ions.

Ethyl 2-cyano-2-(4-nitrophenylsulfonyloxyimino)acetate-mediated Lossen rearrangement: single-pot racemization-free synthesis of hydroxamic acids and ureas from carboxylic acids.

Ethyl 2-cyano-2-(4-nitrophenylsulfonyloxyimino)acetate (4-NBsOXY) mediated Lossen rearrangement and its application for the synthesis of ureas is demonstrated. Required hydroxamic acids for the Lossen rearrangements were synthesized from carboxylic acids using the same reagent. Finally, reaction of an amine with the produced isocyanate resulted in urea. Good yields without racemization were achieved under milder and simpler reaction conditions. Reactions are compatible with common N-protecting groups, such as Boc, Fmoc, Cbz, and benzyl, as well as various OH protecting groups, such as (t)Bu and Bzl. Conversion from carboxylic acid to urea is achieved in one pot. Most importantly, byproducts Oxyma [ethyl 2-cyano-2-(hydroxyimino)acetate] and 4-nitrobenzenesulfonic acid can be recovered easily and can be recycled to prepare the reagent. Thus, the method is environmentally friendly and cost-effective.

Ethyl 2-cyano-2-(2-nitrobenzenesulfonyloxyimino)acetate (o-NosylOXY): a recyclable coupling reagent for racemization-free synthesis of peptide, amide, hydroxamate, and ester.

Ubiquitousness of amide and ester functionality makes coupling reactions extremely important. Although numerous coupling reagents are available, methods of preparation of the common and efficient reagents are cumbersome. Those reagents generate a substantial amount of chemical waste and lack recyclability. Ethyl 2-cyano-2-(2-nitrobenzenesulfonyloxyimino)acetate (o-NosylOXY), the first member of a new generation of coupling reagents, produces byproducts that can be easily recovered and reused for the synthesis of the same reagent, making the method more environmentally friendly and cost-effective. The synthesis of amides, hydroxamates, peptides, and esters using this reagent is described. The synthesis of the difficult sequences, for example, the islet amyloid polypeptide (22-27) fragment (with a C-terminal Gly, H-Asn-Phe-Gly-Ala-Ile-Leu-Gly-NH2) and acyl carrier protein (65-74) fragment (H-Val-Gln-Ala-Ala-Ile-Asp-Tyr-Ile-Asn-Gly-OH), following the solid-phase peptide synthesis (SPPS) protocol and Amyloid ß (39-42) peptide (Boc-Val-Val-IIe-Ala-OMe), following solution-phase strategy is demonstrated. Remarkable improvement is noticed with respect to reaction time, yield, and retention of stereochemistry. A mechanistic investigation and recyclability are also described.

Early events during the aggregation of Aß16-22-derived switch-peptides tracked using Protein Charge Transfer Spectra.

BACKGROUND: Understanding Aß aggregation and inhibiting it at early stages is of utmost importance in treating Alzheimer's and other related amyloidogenic diseases. However, majority of the techniques to study Aß aggregation mainly target the late stages; while those used to monitor early stages are either expensive, use extrinsic dyes, or do not provide information on molecular level interactions. Here, we investigate the early events of Aß16-22(KLVFFAE) aggregation using Aß16-22 derived switch-peptides (SwPs) through a novel label-free approach employing Protein Charge Transfer Spectra (ProCharTS). RESULTS: When pH is increased from 2 to 7.2, the Aß-derived switch peptides undergo controlled self-assembly, where the initial random coil peptides convert into ß-sheet. We leveraged the intrinsic absorbance/luminescence arising from ProCharTS among growing peptide oligomers to observe the aggregation kinetics in real-time. In comparison to monomer, the lysine and glutamate headgroups in the peptide oligomer are expected to come in proximity enhancing ProCharTS intensity due to photoinduced electron transfer. With a combination of Aß-derived switch-peptides and ProCharTS, we obtained structural insights on the early stages of Aß-derived SwP aggregation in four unique peptides. Increase in scatter corrected ProCharTS absorbance (250-500 nm) and luminescence (320-720 nm) along with decreased mean luminescence lifetime (2.3-0.8 ns) characterize the initial stages of aggregation monitored for 1-96 h depending on the peptide. We correlated the results with Circular Dichroism (CD), 8-anilino-1-naphthalenesulfonic acid (ANS) and Thioflavin T (ThT) measurements. SIGNIFICANCE: We demonstrate ProCharTS as an intrinsic analytical probe with following advantages over other conventional methods to track aggregation: it is a label-free probe; it's intensity can be measured using a UV-Vis spectrophotometer; it is more sensitive in detecting the early molecular events in aggregation compared to ANS and ThT; and it can provide information on specific contacts made between charged headgroups of Lysine/Glutamate in the oligomer.

Unprecedented C-C Bond Formation via Ipso Nucleophilic Substitution of 2,4-Dinitrobenzene Sulfonic Acid with Active Methylene Compounds.

The sulfonic acid functionalization of sufficiently electron-deficient benzene sulfonic acids undergoes ipso nucleophilic substitution with various active methylene compounds, leading to new C-C bond formation. Good to excellent yields are obtained under mild conditions without transition-metal (Pd or Cu) catalyst, PTC, and ligand. No solid waste is generated. It is a highly effective strategy for incorporating various active methylene compounds into the o-nitro-substituted benzene ring. This method has been applied not only for synthesizing APIs but also in materials chemistry. It shows a novel route for creating heavily crowded all-carbon quaternary centers. Carbon-carbon bond formation by substituting a sulfonic acid group was unknown.

A proteolytic functional amyloid digests pathogenic amyloids.

Although amyloids are a well-known pathological structure, functional amyloids are beneficial. Functional amyloids can be engineered to cultivate desired functionality that can destroy malicious amyloids. However, not much is known about such amyloid destructors. On the other hand, nearly all approaches to developing a drug against pathogenic amyloidoses have failed. Therefore, novel approaches are needed. Herein, a rationally designed catalytic triad based "proteolytic functional amyloid (PFA)" formed by linking a target protein recognizing unit with a Gly-integrated non-native Glu-His-Cys segment is reported. The proteolytic mechanism of the designed PFA is boosted by thiol/disulfide exchange cleavage. Rigorous MALDI-TOF and FRET-based analyses indicated that the PFAs cleaved Aß12-21 (model Aß) and the pathogenic Aß1-40 site selectively in vitro. PFA significantly inhibited the aggregation of Aß1-40 and broke-down the preformed fibrillar amyloids into non-toxic metabolites. Such a platform may be helpful in not only the on-demand chemical degradation of pathogenic amyloids but also the targeted degradation of other malicious proteins. PFAs are the first "amyloid-destroying" amyloids.

Copper chelating cyclic peptidomimetic inhibits Aß fibrillogenesis.

Misfolding of the amyloid-ß peptide (Aß) and its subsequent aggregation into toxic oligomers is one of the leading causes of Alzheimer's disease (AD). As a therapeutic approach, cyclic peptides have been modified in many ways and developed as a potential class of amyloid aggregation inhibitors. Head-to-tail cyclic peptides with alternating d, l amino acids inhibit amyloid aggregation significantly. On the other hand, excess deposition of copper, iron, and zinc enhances amyloid aggregation. Dysregulation of these metal ions in the brain triggers aggregation by binding to the Aß peptide. Therefore, specific metal chelators have been developed for disrupting the Aß-metal complex, thereby reducing toxicity and restoring metal ion homeostasis. Herein, we report the development of a head-to-tail cyclic peptidomimetic with a copper chelating ligand attached. The designed peptidomimetic inhibits amyloid aggregation significantly in a two-fold molar ratio to the Aß peptide, as confirmed by the thioflavin T (ThT) fluorescence assay, dynamic light scattering (DLS), transmission electron microscopy (TEM), and Congo-red stained birefringence studies. The chelating ligand attached to the cyclic peptide binds efficiently to Cu2+ but weakly to Zn2+ and Fe2+, thereby exhibiting profound selectivity, probed using UV-visible spectroscopy, thioflavin T (ThT) fluorescence assay, tyrosine (TYR10) fluorescence assay, isothermal titration calorimetry (ITC) and transmission electron microscopy (TEM). The non-toxicity of the designed peptidomimetics and their ability to reduce aggregating Aß-fragment induced cytotoxicity was confirmed by the MTT assay on the mouse neuronal cell line. Further, the molecular interaction between the peptidomimetics and the Aß-fragment was confirmed by Förster resonance energy transfer (FRET) studies using fluorescently labeled analogs. Cytotoxicity and cell internalization were also confirmed. A preliminary mechanistic investigation indicates that the peptidomimetic works by a synergistic effect of conformational restriction and metal sequestration. Such peptidomimetics can shed light on the mechanism of aggregation and a novel therapeutic approach.

Protecting Group-Directed Diversity in the Morphology of Self-Assembled Ant-Aib Dipeptides: Garland-Like Architecture and Nanovesicle Formation.

The morphology and molecular organization of a set of different N-terminal protecting groups containing dipeptides were investigated. The dipeptides consisted of two rigid noncanonical amino acids, Ant and Aib (X-Ant-Aib-OMe; Ant: anthranilic acid and 2-aminobenzoic acid, Aib: 2-aminoisobutyric acid). The change of the N-terminal protecting groups (X = Boc (peptide 1), Nα-fluorenylmethoxycarbonyl (Fmoc) (peptide 2), o-NBS (peptide 3), and p-NBS (peptide 4); NBS = nitrobenzyl sulfonyl group) displayed a characteristic morphological variety. Field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM) experiments suggested that while t-butyloxycarbonyl (Boc) and p-NBS containing peptides exhibited distinct rod-like fiber structures, Fmoc and o-NBS containing peptides displayed remarkable vesicular structures. FE-SEM and thermogravimetric analysis (TGA) suggested that peptide nanostructures demonstrated excellent thermal stability in dry conditions. Interestingly, peptides 2 and 4 exhibited a type-III N2 gas adsorption isotherm. Fluorescence microscopy analysis revealed that nanovesicles formed by peptides 2 and 3 have drug encapsulation properties exemplified by curcumin, rhodamine B, and carboxyfluorescein. These results will help in designing peptide-based nanomaterials for diverse applications.

Site-specific single point mutation by anthranilic acid in hIAPP8-37 enhances anti-amyloidogenic activity.

Amylin or hIAPP, together with insulin, plays a significant role in glucose metabolism. However, it undergoes ß-sheet rich amyloid formation associated with pancreatic ß-cell dysfunction leading to type-2 diabetes (T2D). Recent studies suggest that restricting ß-sheet formation in it may halt amyloid formation, which may limit the risk for the disease. Several peptide-based inhibitors have been reported to prevent aggregation. However, most of them have limitations, including low binding efficiency, active only at higher doses, poor solubility, and proteolytic degradation. Insertion of non-coded amino acids renders proteolytically stable peptides. We incorporated a structurally rigid ß-amino acid, Anthranilic acid (Ant), at different sites within the central hydrophobic region of hIAPP and developed two singly mutated hIAPP8-37 peptidomimetics. These peptidomimetics inhibited the amyloid formation of hIAPP substantially even at low concentration, as evident from in vitro ThT, CD, FT-IR, TEM, and Congo red staining birefringence results. These peptidomimetics also disrupted the preformed aggregates formed by hIAPP into non-toxic species. These ß-amino acid-based peptidomimetics can be an attractive scaffold for therapeutic design towards T2D or other protein misfolding diseases.

Total degradation of extracellular amyloids by miniature artificial proteases.

A miniaturized mimic of the active site of a protease, chymotrypsin, was linked to a target recognition unit to generate "Miniature Artificial Proteases" (mAPs). Time-resolved MALDI-TOF data analyses indicated that mAPs cleaved every amide bond between Lys16-Phe20 of the amyloid ß fragment (Aß12-21) and Aß1-40, resulting in inhibition of fibrillization and disruption of the preformed amyloid. Such a platform may offer not only new therapeutic options against various amyloidoses but also novel routes for the selective knockdown of specific proteins.

Peptidomimetics prepared by tail-to-side chain one component peptide stapling inhibit Alzheimer's amyloid-ß fibrillogenesis.

Alzheimer's disease (AD) is the most common form of dementia affecting the elderly population worldwide. Despite enormous efforts and considerable advancement in research, no therapeutic agents have come to light to date. However, many peptide-based and small molecule inhibitors interact efficiently with the amyloid-ß (Aß) peptide and alter its aggregation pathway. On the other hand, stapled peptides have been developed mainly to stabilize α-helix conformations and study protein-protein interactions. ß-Sheet stabilization or destabilization by stapled peptides has not been explored enough. Herein, we describe the generation of a library of "tail-to-side chain" stapled peptides via lactamization and their application for the first time as modulators of Aß1-40 self-association and fibrillogenesis. They also disrupt the preformed fibrillar aggregates into nontoxic species. Their stability in the presence of proteolytic enzymes is increased due to stapling. Therefore, the stapled peptides thus formed can be useful as potent amyloid aggregation inhibitors and pave a therapeutic pathway for combating amyloid-related diseases. Also, they may help in gaining insight into the process of aggregation.

An explicitly designed paratope of amyloid-ß prevents neuronal apoptosis in vitro and hippocampal damage in rat brain.

Synthetic antibodies hold great promise in combating diseases, diagnosis, and a wide range of biomedical applications. However, designing a therapeutically amenable, synthetic antibody that can arrest the aggregation of amyloid-ß (Aß) remains challenging. Here, we report a flexible, hairpin-like synthetic paratope (SP1, ∼2 kDa), which prevents the aggregation of Aß monomers and reverses the preformed amyloid fibril to a non-toxic species. Structural and biophysical studies further allowed dissecting the mode and affinity of molecular recognition events between SP1 and Aß. Subsequently, SP1 reduces Aß-induced neurotoxicity, neuronal apoptosis, and ROS-mediated oxidative damage in human neuroblastoma cells (SH-SY5Y). The non-toxic nature of SP1 and its ability to ameliorate hippocampal neurodegeneration in a rat model of AD demonstrate its therapeutic potential. This paratope engineering module could readily implement discoveries of cost-effective molecular probes to nurture the basic principles of protein misfolding, thus combating related diseases.

Engineered peptidic constructs metabolize amyloid ß by self-assembly-driven reactions.

Inspired by the unique mechanism of proteolytic maturation of host cell factor-1, we designed small peptide-based constructs that selectively recognized amyloid ß (Aß) and cleaved it in a non-catalytic manner initially around the α-secretase cleavage-site, thus termed as "artificial α-secretases". "Artificial α-secretases" also cleaved Aß on the cleavage-sites of other Aß processing enzymes by prolonged treatment, as evidenced by time-resolved MALDI-TOF-mass analyses.

Synthesis of o-Nitroarylamines via Ipso Nucleophilic Substitution of Sulfonic Acids.

A mild, efficient, and eco-friendly method for the synthesis of o-nitroarylamine from o-nitroaryl sulfonic acid via ipso nucleophilic aryl substitution by amine is described. The products have been obtained with good yields at room temperature without the assistance of any metal, activating agent, or toxic oxidant. This method is useful for racemization-free synthesis of N-aryl amino acid esters.

A Synthetic Pro-Drug Peptide Reverses Amyloid-ß-Induced Toxicity in the Rat Model of Alzheimer's Disease.

BACKGROUND: Alzheimer's disease (AD), the most prevalent neurodegenerative disorder, involves the formation of the extracellular amyloid-ß (Aß) plaques and intracellular neurofibrillary tangles. The current therapies against AD are symptomatic with limited benefits but associated with major side effects. Inhibition of self-aggregation of Aß peptides into higher order cross-ß structure is one of the potential therapeutic approach which may counter oligomerization of Aß peptide. OBJECTIVE: The present study aimed to evaluate the neuroprotective and anti-inflammatory potential of a synthetic Pro-Drug type peptide (PDp) against Aß-induced toxicity in rat model of AD. METHODS: Intra-hippocampal microinjection of toxic Aß40 (IHAß40) by stereotaxic surgery was performed in the male Sprague-Dawley rats to generate an Aß-induced AD model. Sub-chronic toxicity of synthetic PDp using hematological, biochemical, and histopathological parameters was investigated. Evaluation of PDp on Aß-induced neurodegeneration and neuroinflammation was performed. RESULTS: PDp inhibits plaque formation with increase in Nissl granule staining in the rat hippocampus. Aß-induced toxicity associated imbalance in reactive oxygen species and antioxidant enzymes activity such as superoxide dismutase and catalase in the rat brain was overcome by PDp treatment. Tau protein hyperphosphorylation was normalized with PDp treatment. Also, the neuroinflammatory response was suppressed with PDp treatment. CONCLUSION: The present study depicts the potential neuroprotective role of PDp against Aß-induced toxicity in rat. PDp inhibits plaque formation thereby normalizing oxidative stress, inhibiting tau protein hyperphosphorylation, and suppressing neuroinflammatory responses. Future studies done in this direction will pave way for new therapeutic strategies.

Sequence specificity of amylin-insulin interaction: a fragment-based insulin fibrillation inhibition study.

Subcutaneous insulin delivery serves as the major treatment for the ever-increasing spread of type II diabetes worldwide. However, long-term exposure to insulin results in local aggregates at the site of injection. This therapeutic concern accentuates the need to develop newer effective excipients to stabilize the insulin in pharmaceutical formulations. The fact that in normal physiological conditions, insulin interacts with the amylin hormone co-secreted from the pancreas, we targeted a peptide-mimetic approach based on the amylin sequence. The amylin-fibrillating core (NL6- N22FGAIL27 from the human Islet Amyloid Poly-Peptide) and its derivative NFGAXL (NL6X, X = 2-aminobenzoic acid) were used as potential inhibitory peptides against insulin amyloidogenesis. The fibrillation kinetics in the presence of the inhibitors was studied using an array of biophysical and microscopic techniques. High-resolution NMR spectroscopy enabled probing of the inhibitory interaction at an atomic resolution. Our results highlight the potential of using the naturally evolved NL6 peptide as an effective inhibitor against insulin fibrillation.

Switch-peptides: design and characterization of controllable super-amyloid-forming host-guest peptides as tools for identifying anti-amyloid agents.

Several amyloid-forming proteins are characterized by the presence of hydrophobic and highly amyloidogenic core sequences that play critical roles in the initiation and progression of amyloid fibril formation. Therefore targeting these sequences represents a viable strategy for identifying candidate molecules that could interfere with amyloid formation and toxicity of the parent proteins. However, the highly amyloidogenic and insoluble nature of these sequences has hampered efforts to develop high-throughput fibrillization assays. Here we describe the design and characterization of host-guest switch peptides that can be used for in vitro mechanistic and screening studies that are aimed at discovering aggregation inhibitors that target highly amyloidogenic sequences. These model systems are based on a host-guest system where the amyloidogenic sequence (guest peptide) is flanked by two beta-sheet-promoting (Leu-Ser)(n) oligomers as host sequences. Two host-guest peptides were prepared by using the hydrophobic core of Abeta comprising residues 14-24 (HQKLVFFAEDV) as the guest peptide with switch elements inserted within (peptide 1) or at the N and C termini of the guest peptide (peptide 2). Both model peptides can be triggered to undergo rapid self-assembly and amyloid formation in a highly controllable manner and their fibrillization kinetics is tuneable by manipulating solution conditions (for example, peptide concentration and pH). The fibrillization of both peptides reproduces many features of the full-length Abeta peptides and can be inhibited by known inhibitors of Abeta fibril formation. Our results suggest that this approach can be extended to other amyloid proteins and should facilitate the discovery of small-molecule aggregation inhibitors and the development of more efficacious anti-amyloid agents to treat and/or reverse the pathogenesis of neurodegenerative and systemic amyloid diseases.

(E)-Ethyl-2-cyano-2-(((2,4,6-trichlorobenzoyl)oxy)imino)acetate: A Modified Yamaguchi Reagent for Enantioselective Esterification, Thioesterification, Amidation, and Peptide Synthesis.

Here, the synthesis and applications of (E)-ethyl-2-cyano-2-(((2,4,6-trichlorobenzoyl)oxy)imino)acetate as a racemization suppressing and easily recyclable version of the Yamaguchi reagent that can be used for amide and peptide synthesis are reported. We demonstrated its application in racemization-free esterification, thioesterification, amidation, and peptide bond formation. We successfully synthesized oligopeptides on the solid support in dimethylformamide as well as in solution (dichloromethane) by applying this coupling reagent. It is important to note that a mixed-anhydride-based method provides peptide-forming reactions as good as the current methods using built-in coupling reagents. Mechanism investigation, racemization suppression, and recyclability are also discussed.