Metal-mediated Peptide Assembly: Use Of Metal Coordination To Change The Oligornerization State Of An Alpha-helical Coiled-coil

Metal coordination is used to alter the oligomerization state of a designed peptide structure. The 30-residue polypeptide AQ-Pal21 4Pal21 contains two metal-binding 4-pyridylalanine (Pal) residues on its solvent-exposed surface and exists as a very stable two-stranded a-helical coiled-coil. Upon the addition of Pt(en)(NO3)(2), a significant conformational change to a metal-bridged, four-helix bundle is seen

Formation Of Peptide Nanospheres And Nanofibrils By Metal Coordination

Two amphipathic polypeptides were coordinated to the cis positions of a square planar Pt(II) complex in order to provide the metal center with two noncovalent oligomerization domains. This resulted in the formation of new metal-peptide nanoassemblies which are shown to exist as nanometer-sized spheres and fibrils. Construction of these assemblies was based on the 30-residue polypeptide AQ-Pal14 which was designed for its ability to self-assemble into the common protein oligomerization motif of a noncovalent coiled-coil, and modified to contain a metal-binding 4-pyridylalanine residue at its surface. When AQ-Pal14 was reacted with Pt(en)(NO3)(2), a new metal-peptide complex was formed in which two AQ-Pal14 peptides were coordinated to a single metal center as determined by sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) and electrospray ionization mass spectrometry (ESI-MS). When the reaction mixture was analyzed under nondenaturing conditions by high performance size exclusion chromatography (HPSEC), it was found that all species present eluted at the column void volume, indicating the formation of very large metal-peptide assemblies. This was verified by multiangle light scattering (MALS) which showed that the metal-peptide assemblies have a weight-averaged molecular mass and z-average root-mean-square radius of M-W = (7 +/- 4) x 10(6) g/mol and R-Z = 18 +/- 4 nm, respectively. The presence of such nanometer scale assemblies was confirmed by transmission electron microscopy and atomic force microscopy which showed the existence of both spherical and fibrillar nanostructures

Plant Coumarins with Anti-HIV Activity: Isolation and Mechanisms of Action

This review summarizes and systematizes the literature on the anti-HIV activity of plant coumarins with emphasis on isolation and the mechanism of their antiviral action. This review summarizes the information on the anti-HIV properties of simple coumarins as well as annulated furano- and pyranocoumarins and shows that coumarins of plant origin can act by several mechanisms: inhibition of HIV reverse transcriptase and integrase, inhibition of cellular factors that regulate HIV-1 replication, and transmission of viral particles from infected macrophages to healthy ones. It is important to note that some pyranocoumarins are able to act through several mechanisms or bind to several sites, which ensures the resistance of these compounds to HIV mutations. Here we review the last two decades of research on the anti-HIV activity of naturally occurring coumarins

Nano-biosupercapacitors enable autarkic sensor operation in blood

Today’s smallest energy storage devices for in-vivo applications are larger than 3 mm3 and lack the ability to continuously drive the complex functions of smart dust electronic and microrobotic systems. Here, we create a tubular biosupercapacitor occupying a mere volume of 1/1000 mm3 (=1 nanoliter), yet delivering up to 1.6 V in blood. The tubular geometry of this nano-biosupercapacitor provides efficient self-protection against external forces from pulsating blood or muscle contraction. Redox enzymes and living cells, naturally present in blood boost the performance of the device by 40% and help to solve the self-discharging problem persistently encountered by miniaturized supercapacitors. At full capacity, the nano-biosupercapacitors drive a complex integrated sensor system to measure the pH-value in blood. This demonstration opens up opportunities for next generation intravascular implants and microrobotic systems operating in hard-to-reach small spaces deep inside the human body

Express method for isolation of ready-to-use 3D chitin scaffolds from aplysina archeri (aplysineidae: verongiida) demosponge

Sponges are a valuable source of natural compounds and biomaterials for many biotechnological applications. Marine sponges belonging to the order Verongiida are known to contain both chitin and biologically active bromotyrosines. Aplysina archeri (Aplysineidae: Verongiida) is well known to contain bromotyrosines with relevant bioactivity against human and animal diseases. The aim of this study was to develop an express method for the production of naturally prefabricated 3D chitin and bromotyrosine-containing extracts simultaneously. This new method is based on microwave irradiation (MWI) together with stepwise treatment using 1% sodium hydroxide, 20% acetic acid, and 30% hydrogen peroxide. This approach, which takes up to 1 h, made it possible to isolate chitin from the tube-like skeleton of A. archeri and to demonstrate the presence of this biopolymer in this sponge for the first time. Additionally, this procedure does not deacetylate chitin to chitosan and enables the recovery of ready-to-use 3D chitin scaffolds without destruction of the unique tube-like fibrous interconnected structure of the isolated biomaterial. Furthermore, these mechanically stressed fibers still have the capacity for saturation with water, methylene blue dye, crude oil, and blood, which is necessary for the application of such renewable 3D chitinous centimeter-sized scaffolds in diverse technological and biomedical fields. © 2019 by the authors

Naturally drug-loaded chitin: Isolation and applications

Naturally occurring three-dimensional (3D) biopolymer-based matrices that can be used in different biomedical applications are sustainable alternatives to various artificial 3D materials. For this purpose, chitin-based structures from marine sponges are very promising substitutes. Marine sponges from the order Verongiida (class Demospongiae) are typical examples of demosponges with well-developed chitinous skeletons. In particular, species belonging to the family Ianthellidae possess chitinous, flat, fan-like fibrous skeletons with a unique, microporous 3D architecture that makes them particularly interesting for applications. In this work, we focus our attention on the demosponge Ianthella flabelliformis (Linnaeus, 1759) for simultaneous extraction of both naturally occurring (“ready-to-use”) chitin scaffolds, and biologically active bromotyrosines which are recognized as potential antibiotic, antitumor, and marine antifouling substances. We show that selected bromotyrosines are located within pigmental cells which, however, are localized within chitinous skeletal fibers of I. flabelliformis. A two-step reaction provides two products: treatment with methanol extracts the bromotyrosine compounds bastadin 25 and araplysillin-I N20 sulfamate, and a subsequent treatment with acetic acid and sodium hydroxide exposes the 3D chitinous scaffold. This scaffold is a mesh-like structure, which retains its capillary network, and its use as a potential drug delivery biomaterial was examined for the first time. The results demonstrate that sponge-derived chitin scaffolds, impregnated with decamethoxine, effectively inhibit growth of the human pathogen Staphylococcus aureus in an agar diffusion assa

Spider chitin: An Ultrafast Microwave-Assisted Method for Chitin Isolation from Caribena versicolor Spider Molt Cuticle

Chitin, as a fundamental polysaccharide in invertebrate skeletons, continues to be actively investigated, especially with respect to new sources and the development of effective methods for its extraction. Recent attention has been focused on marine crustaceans and sponges; however, the potential of spiders (order Araneae) as an alternative source of tubular chitin has been overlooked. In this work, we focused our attention on chitin from up to 12 cm-large Theraphosidae spiders, popularly known as tarantulas or bird-eating spiders. These organisms “lose” large quantities of cuticles during their molting cycle. Here, we present for the first time a highly effective method for the isolation of chitin from Caribena versicolor spider molt cuticle, as well as its identification and characterization using modern analytical methods. We suggest that the tube-like molt cuticle of this spider can serve as a naturally prefabricated and renewable source of tubular chitin with high potential for application in technology and biomedicine. © 2019 by the authors

Design and Development of Metal-Peptide Nanoscaled Materials

The work presented in this dissertation demonstrates how de-novo designed peptides having the double stranded á-helical coiled-coil conformation can be organized into molecular assemblies by metal coordination. The design of these peptides explores the positioning of a strong metal binding site, 4-pyridylalanine, within the hydrophilic portion of the peptides in order to coordinate the metal complexes into well-defined geometries. The effect of the peptide’s sequence on the stability of the formed metal-peptide complex has been shown through the reaction of Pal14 and Pal14n with ethylenediamine platinum (II). In particular, it was found that peptides based on an IEALEGK repeat do not form stable metals complexes. In contrast, peptides based on an IAALEQK repeat do form stable platinum complexes which in water assemble into globular structures that are 40 nm in diameter. Incorporation of a covalent crosslink into the Pal14n coiled-coil structure (Pal14C19nox) forces this peptide to form linear assemblies after the reaction with the platinum complex. The last chapter of this dissertation reveals that multiple metal binding sites on the hydrophilic exterior of the two-stranded coiled-coil Pal14Pal21n forces the formation of cyclic tetramers, rather then a polymeric product. It was also found that the conformational “plasticity” of the non-covalent coiled coil Pal14Pal21n is necessary for the formation of the platinum-peptide tetramer. In contrast, the covalently “secured” coiled-coil structure of Pal14C19Pal21nox restricts conformation changes within the molecule, which inhibits the platinum complex from orienting the peptide ligand in order to form the tetramer structure

Antiviral Potential of <i>Antillogorgia americana</i> and <i>elisabethae</i> Natural Products against nsp16–nsp10 Complex, nsp13, and nsp14 Proteins of SARS-CoV-2: An In Silico Investigation

Biomolecules of marine origin have many applications in the field of biotechnology and medicine, but still hold great potential as bioactive substances against different diseases. The purification or total synthesis of marine metabolites is expensive, and requires a reliable selection method to reveal their pharmaceutical potential prior to clinical validation. This study aimed to explore the hidden potential of natural products from the gorgonian genus Antillogorgia as anti-SARS-CoV-2 agents, via binding affinity assessments and molecular dynamics (MDs) simulations. The three-dimensional protein structures of the nsp16–nsp10 complex, nsp13, and nsp14 were acquired from the RCSB PDB database. All 165 natural products (NPs) were discovered using the PubChem, ChemSpider, and CMNPD databases. The freeware Autodock Vina was used to conduct the molecular docking procedure, once the proteins and ligands were prepared using BIOVIA discovery studio and Avogadro software v1.95. Before running MDs simulations using the CABS-flex 2.0 website, the binding affinity assessments and amino acid interactions were carefully examined. Just twelve NPs were selected, and five of those NPs interacted optimally with the catalytic amino acids of proteins. To conclude, pseudopterosin A (−8.0 kcal/mol), seco-pseudopterosin A (−7.2 kcal/mol), sandresolide B (−6.2 kcal/mol), elisabatin A (−7.0 kcal/mol), and elisapterosin A (−10.7 kcal/mol) appeared to be the most promising candidates against the nsp16–nsp10, nsp13, and nsp14 proteins

Natural Products from Red Algal Genus <i>Laurencia</i> as Potential Inhibitors of RdRp and nsp15 Enzymes of SARS-CoV-2: An In Silico Perspective

The genus Laurencia, a category of marine red algae, is well recognized for producing a large variety of natural products (NPs) that are both chemically intriguing and structurally distinct. The aim of this research was to identify NPs with potential anti-SARS-CoV-2 activity. The crystals of the proteins RdRp and nsp15 were obtained from the RCSB protein database. About 300 NPs were discovered using the PubChem, ChemSpider, and CMNPD databases. The program Autodock Vina was used to conduct the molecular docking procedure once the proteins and ligands were prepared. Before running MD simulations using the CABS-flex 2.0 website, binding affinity assessments and interactions between amino acids were carefully reviewed. Only nine NPs were shortlisted to be examined further. Bromophycolide R, S, and bromophycoic acid C show the tendency to inhibit RdRp by β-hairpin motif binding at the N-terminal known as Active site 2 (AS2), whereas the other four NPs, bromophycolide E, H, P, and thyrsenol A, may effectively inhibit RdRp through interactions via C-terminal, also known as the Active site 1 (AS1). For the enzyme nsp15, bromophycoic B, C, and floridoside showed plausible interactions. In conclusion, out of nine, seven candidates shortlisted for RdRp exhibited strong interactions with the key residues in the AS1 and AS2 regions. Bromophycoic acid C may work as a dual inhibitor due to its favorable interactions with the nsp15 protein and RdRp’s N-terminal, with affinities of −8.5 and −8.2 kcal/mol, respectively