De novo designed aliphatic and aromatic peptides assemble into amyloid-like cytotoxic supramolecular nanofibrils.

Peptides are very interesting biomolecules that upon self-association form a variety of thermodynamically stable supramolecular structures of nanometric dimension e.g. nanotubes, nanorods, nanovesicles, nanofibrils, nanowires and many others. Herein, we report six peptide molecules having a general chemical structure, H-Gaba-X-X-OH (Gaba: γ-aminobutyric acid, X: amino acid). Out of these six peptides, three are aromatic and the others are aliphatic. Atomic force microscopic (AFM) studies reveal that except peptide 6 (H-Gaba-Trp-Trp-OH), all the reported peptides adopt nanofibrillar morphology upon aggregation in aqueous medium. These supramolecular assemblies can recognize amyloid-specific molecular probe congo red (CR) and thioflavine t (ThT) and exhibit all the characteristic properties of amyloids. The MTT cell viability assay reveals that the toxicity of both aliphatic and aromatic peptides increases with increasing concentration of the peptides to both cancer (HeLa) and non-cancer (HEK 293) cells. Of note, the aromatic peptides show a slightly higher cytotoxic effect compared to the aliphatic peptides. Overall, the studies highlight the self-assembling nature of the de novo designed aliphatic and aromatic peptides and pave the way towards elucidating the intricacies of pathogenic amyloid assemblies.

Ecological safety with multifunctional applications of biogenic mono and bimetallic (Au-Ag) alloy nanoparticles.

Recently, the design and biosynthesis of metallic nanoparticles (NPs) have drawn immense interest, but their very specific function and secondary toxic effects are major concern towards commercial application of NPs. That's why environment-friendly (nontoxic) NPs having multiple functions are extremely important. Herein, we report the mechanism of biosynthesis of mono and bimetallic (Au-Ag) alloy NPs and study their multifunctional (antioxidant, antifungal and catalytic) activity and ecotoxicological property. AgNPs exhibit phytotoxicity (at 100 µg/ml) on morphological characteristics of Lentil (during germination), while alloy and AuNPs are non-toxic (up to 100 µg/ml). In-vitro antioxidant response using DPPH methods reveals that alloy NPs (IC50 = 55.8 µg/ml) possesses better antioxidant activity compared to the monometallic NPs (IC50 = 73.6-82.6 µg/ml). In addition, alloy NPs displayed appreciable antifungal efficacy against a plant pathogenic fungus Gloeosporium musarum by structural damage to hyphae and conidia of the fungus. The catalytic performance of NPs for degradation of chlorpyriphos (CP) pesticide reveals that alloy NPs is more efficient in terms of rate constant (k = 0.405 d-1) and half-life (T50 = 1.71 d) compared to the monometallic counterparts (k = 0.115-0.178 d-1; T50 = 3.89-6.04 d). Degradation products of CP (3,5,6-trichloropyridinol and diethyl thiophosphate) are confirmed using mass spectrometry and based on that a degradation pathway has been suggested. Thus, these sustainable and ecological safe biogenic (Au-Ag) alloy NPs promise multiple applications as an antioxidant in the pharmaceutical sector, as a fungicide for disease control in agriculture, as a catalyst for remediation of toxic pollutants and in other pertinent areas.

Poly C Binding Protein 2 dependent nuclear retention of the utrophin-A mRNA in C2C12 cells.

Upregulation of utrophin, the autosomal homologue of dystrophin, can compensate dystrophin deficiency in Duchenne Muscular Dystrophy (DMD) although the therapeutic success is yet to be achieved. The present study has identified Poly (C) binding protein 2 (PCBP2) as a post-transcriptional suppresser for the expression of utrophin-A, the muscle-specific utrophin isoform. This study confirms nuclear retention of utrophin-A mRNA in C2C12 cells, which is mediated by PCBP2. Further investigation demonstrates PCBP2-dependent nuclear retention of follistatin mRNA as well. Its involvement in nuclear retention of mRNA sheds light on a novel function of PCBP2 that makes utrophin-A mRNA less available in cytosol. PCBP2, therefore, may be a target to de-repress utrophin-A expression in DMD.

Author Correction: Process optimization for biosynthesis of mono and bimetallic alloy nanoparticle catalysts for degradation of dyes in individual and ternary mixture.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Process optimization for biosynthesis of mono and bimetallic alloy nanoparticle catalysts for degradation of dyes in individual and ternary mixture.

Nanoparticle (NP) catalysts are widely used for removal of dyes for single use, but there is an acute need for developing catalysts with high efficiency and reusability for mixed dyes. Here we first optimized the process (reactant proportion, temperature, time, and pH) for biosynthesis of monometallic Ag, Au and bimetallic Au-Ag alloy NP catalysts using Polyalthia longifolia leaf extract. The biosynthesized NP catalysts were characterized by UV-vis, DLS, Zeta potential, TEM and EDX study while the probable biomolecules responsible for biosynthesis were identified by FTIR and GC-MS/MS analysis. The NPs are found to be mostly spherical in shape (size 5-20 nm) with prolonged stability. We evaluated their chemo-catalytic performance through degradation of dyes (methyl orange, methyl violet, methylene blue) in individual and ternary mixture in presence of NaBH4. The degradation percentage (80.06-96.59% within 5 min), degradation kinetics (k = 0.361-1.518 min-1), half-life (T50 = 0.457-1.920 min) and 80% degradation (T80 = 1.060-4.458 min) of dyes indicated highest catalytic activity of alloy in ternary mixture. Here we report a unique vacuum filtration system using alloy coated beads with excellent catalytic activity which could be reused thrice for removal of hazardous ternary mixed dyes with great promise for environmental remediation.

Targeting G-quadruplex DNA with synthetic dendritic peptide: modulation of the proliferation of human cancer cells.

Telomerase, a reverse transcriptase enzyme, is found to over express in most cancer cells. It elongates the telomere region by repeated adding of TTAGGG in the 3'-end and leads to excess cell proliferation which causes cancer. G-quadruplex (G4) formation can inhibit such telomere lengthening. So, stabilization of G4 structure as well as inhibition of telomerase activity is very promising approach in targeted cancer therapy. Herein, the aptitude of a synthetic dendritic peptide, C δ2-(YEE)-E (peptide 1), to target specifically the human telomeric G4 DNA, dAGGG(TTAGGG)3, has been evaluated. Both biochemical and biophysical techniques including gel mobility shift assay, isothermal titration calorimetry and fluorescence spectroscopy have been employed for the purpose. Circular dichroism study reveals that the targeting results an increase in thermal stability of G4 DNA. Interestingly, replacement of N-terminal tyrosine residue of peptide 1 by valine, C δ2-(VEE)-E, (peptide 2) consequences in loss of its G4 DNA targeting ability, although both the peptides exhibit comparable affinity toward double-stranded DNA. Of note, peptide 1 causes cessation of growth of human cancer cells (HeLa and U2OS) and induces apoptosis in vitro. But it has no significant inhibitory effect on the growth of normal human embryonic kidney 293 cells. Mechanistically, Telomeric Repeat Amplification Protocol (TRAP) assay indicates that peptide 1 effectively inhibits the telomerase activity in human cell extracts. Overall, this study demonstrates the usefulness of a synthetic dendritic peptide as an inhibitor of tumor cell growth by inducing apoptosis upon targeting the telomeric G4 DNA.

Engineering of Supramolecular ß-Sheet and Nontoxic Amyloid Fibrils from Synthetic Oligopeptides Containing γ-Aminobutyric Acid as the N-Terminal Residue.

Here we demonstrate that three synthetic tripeptides containing conformationally flexible γ-aminobutyric acid (γ-Abu) as the N-terminal residue form supramolecular ß-sheet and nanofibrillar aggregates upon self-association in aqueous medium. Congo red and thioflavin T binding study establish that these nanofibrillar aggregates are amyloidogenic in nature. The MTT cell survival assay suggests that these amyloid-like nanofibrillar aggregates are nontoxic toward cultured Neuro 2A cells. Interestingly, none of these tripeptides bear sequence identity with any amyloid forming proteins or peptides; however upon self-association, they form supramolecular ß-sheet and amyloid-like nanofibrils those are nontoxic in nature. The results highlight the self-assembling nature of the conformationally flexible peptides in aqueous environment and support the hypothesis that amyloid formation is the intrinsic property of the polypeptide chain. Also the cytotoxicity is not predictive from amyloid fibril formation alone. Such nontoxic amyloid fibrils can be exploited in future to design functional biomaterials for various biomedical applications.

Molecular recognition of double-stranded DNA by a synthetic, homoaromatic tripeptide (YYY): The spectroscopic and calorimetric study.

The intermolecular interactions of a homoaromatic tripeptide, H-Tyr-Tyr-Tyr-OH (YYY) with model double-stranded (ds) DNA (ct-DNA) have been investigated by isothermal titration calorimetric (ITC) method along with various biophysical techniques such as fluorescence, time correlated single photon counting (TCSPC) and circular dichroism (CD) spectroscopy. The binding affinity [log (K) at 25 °C] of the YYY to ct-DNA is calculated as ≈4.3. The binding mode of the YYY to ds-DNA is elucidated by fluorescence intercalator displacement (FID) assay, melting temperature analysis, viscosity measurement and salt-induced fluorescence quenching study. The studies establish that the YYY recognizes the groove of the ct-DNA. The temperature dependent ITC studies show that the binding interaction is thermodynamically favourable. The compensation between enthalpy and entropy leads to the overall Gibbs free energy change almost invariant. Finally, the generality of the YYY to recognize ds-DNA has been analyzed with other model ds-DNA, ds26, which reveals almost similar binding affinity of the YYY as ct-DNA. The studies elucidate both the spectroscopic and calorimetric insight of the interactions of a homoaromatic tripeptide with ds-DNA and hold the promise of future applications as DNA targeting drug.

Insight into the binding of a non-toxic, self-assembling aromatic tripeptide with ct-DNA: Spectroscopic and viscositic studies.

The report describes the synthesis, self-association and DNA binding studies of an aromatic tripeptide H-Phe-Phe-Phe-OH (FFF). The peptide backbone adopts ß-sheet conformation both in solid and solution. In aqueous solution, FFF self-assembles to form nanostructured aggregates. Interactions of this peptide with calf-thymus DNA (ct-DNA) have been studied using various biophysical techniques including ultraviolet (UV) absorption spectroscopy, fluorescence spectroscopy and circular dichroism (CD) spectroscopy. The value of mean binding constant calculated from UV and fluorescence spectroscopic data is (2.914 ± 0.74) x 103 M-1 which is consistent with an external binding mode. Fluorescence intercalator displacement (FID) assay, iodide quenching study, viscosity measurement and thermal denaturation study of DNA further confirm the groove binding mode of peptide, FFF with ct-DNA. MTT cell survival assay reveals very low cytotoxicity of the peptide toward human lung carcinoma cell line A549.

Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive ß-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data.

Self-assembling dipeptide-based nontoxic vesicles as carriers for drugs and other biologically important molecules.

Self-assembling short peptides can offer an opportunity to make useful nano-/microstructures that find potential application in drug delivery. We report here the formation of multivesicular structures from self-assembling water-soluble synthetic amphiphilic dipeptides containing a glutamic acid residue at the C-terminus. These vesicular structures are stable over a wide range of pH (pH 2-12). However, they are sensitive towards calcium ions. This causes the rupturing of these vesicles. Interestingly, these vesicles can not only encapsulate an anticancer drug and a fluorescent dye, but also can release them in the presence of calcium ions. Moreover, these multivesicular structures have the potential to carry biologically important molecules like cyclic adenosine monophosphate (cAMP) within the cells keeping their biological functions intact. A MTT cell-survival assay suggests the almost nontoxic nature of these vesicles. Thus, these peptide vesicles can be used as biocompatible delivery vehicles for carrying drugs and other bioactive molecules.

Concentration dependent transformation of oligopeptide based nanovesicles to nanotubes and an application of nanovesicles.

The concentration dependent transformation of an oligopeptide nanostructure from nanovesicles to nanotubes at neutral pH is presented. The oligopeptide Acp-Tyr-Glu (Acp: 6-aminohexanoic acid) forms nanovesicles at a concentration of 6.9 mg mL(-1). At a concentration of 2.3 mg mL(-1) these vesicular structures completely disappear and nanotubular structures are observed. We have also successfully optimized an intermediate concentration (3.4 mg mL(-1)) where an ordered array of fused vesicular structures are formed, which actually leads to the transition from nanovesicles to nanotubes. These vesicular structures are very much sensitive toward metal ions and pH. Biocompatible calcium ions and high pH (10.7) can trigger the rupturing of these nanovesicles. One important property of these nanovesicular structures is the encapsulation of a potent anticancer drug doxorubicin, which can also be released in the presence of calcium ions promising a future use of these nanovesicles as vehicles for carrying biologically important molecules.

Tetrapeptide-based hydrogels: for encapsulation and slow release of an anticancer drug at physiological pH.

Here, we report two synthetic oligopeptide-based, thermoreversible, pH-sensitive hydrogels. In gel phase, these self-assembling tetrapeptides form a long interconnected nanofibrilar network structure, as is evident from various microscopic techniques, including field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM). FTIR, circular dichroism, and wide angle X-ray diffraction (WAXD) favor an antiparallel beta-sheet structure of these gelators in the gel state. Finally, these hydrogels have been utilized for entrapment and slow release of an anticancer drug doxorubicin at physiological pH, promising their future application as a drug delivery vehicle.

Water-soluble tripeptide Abeta (9-11) forms amyloid-like fibrils and exhibits neurotoxicity.

A water-soluble, hydrophilic tripeptide GYE, having sequence identity with the N-terminal segment of amyloid peptides Abeta(9-11), upon self-association exhibits amyloid-like fibrils and significant neurotoxicity towards the Neuro2A cell line. However, the tripeptides GFE and GWE, in which the centrally located tyrosine residue has been replaced by phenylalanine or tryptophan, fail to show amyloidogenic behavior and exhibit little or no neurotoxicity.