Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks.

Peptides are promising drug development frameworks that have been hindered by intrinsic undesired properties including hemolytic activity. We aim to get a better insight into the chemical space of hemolytic peptides using a novel approach based on network science and data mining. Metadata networks (METNs) were useful to characterize and find general patterns associated with hemolytic peptides, whereas Half-Space Proximal Networks (HSPNs), represented the hemolytic peptide space. The best candidate HSPNs were used to extract various subsets of hemolytic peptides (scaffolds) considering network centrality and peptide similarity. These scaffolds have been proved to be useful in developing robust similarity-based model classifiers. Finally, using an alignment-free approach, we reported 47 putative hemolytic motifs, which can be used as toxic signatures when developing novel peptide-based drugs. We provided evidence that the number of hemolytic motifs in a sequence might be related to the likelihood of being hemolytic.

Cellulose-based hydrogels towards an antibacterial wound dressing.

Hydrogels are promising candidates for wound healing bandages because they can mimic the native skin microenvironment. Additionally, there is increasing growth in the use of naturally derived materials and plant-based biomaterials to produce healthcare products with healing purposes because of their biocompatibility and biodegradation properties. In this study, cellulose extracted from biodiverse sources in Ecuador was used as the raw material for the fabrication of hydrogels with enhanced antifouling properties. Fourier-transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), and scanning electron microscopy (SEM) were used to characterize the cellulose and hydrogels. In vitro and ex vivo tests were performed to evaluate the antimicrobial activity of hydrogels against Gram-negative bacteria as a model. Finally, the hydrogel synthesized with cellulose extracted from pitahaya showed improved antibacterial activity when applied over pigskin as a proof of concept for wound dressing. Therefore, the present results suggest that cellulose-based hydrogels are good candidates for application as wound dressings.

Photochemical Optimization of a Silver Nanoprism/Graphene Oxide Nanocomposite's Antibacterial Properties.

Optimizing the antibacterial properties of nanocomposites is a fundamental challenge for many biomedical applications. Here, we study how we may optimize the antibacterial activity of narrow-sized anisotropically flat silver nanoprisms (S-NPs) on graphene oxide (GO) against Escherichia coli. To do so, we transformed silver nanoparticles (AgNPs) into S-NPs and anchored them to GO via a facile and low-cost photochemical reduction method by varying the irradiation wavelength during the synthesis process in the visible range (440 to 650 nm and white light). We performed a physicochemical characterization of the resulting S-NP/GO nanocomposite using a combination of UV-vis spectroscopy, X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Our results reveal a synergistic effect between the silver nanoprism and the oxygen functional groups of the GO surface. The antibacterial activity of the S-NPs/GO nanocomposite shows a significantly higher 53% inhibition efficiency after being irradiated with a 540 nm wavelength light source, compared to AgNPs with a 1% inhibition efficiency, respectively. In so doing, we have demonstrated the utility of a low-cost photoreduction method to control the structural properties of silver nanoprism on GO and, in this way, enhance the antibacterial properties of the nanocomposite. These results should be of great interest in a wide range of biomedical applications and medical devices.

Marine Arthropods as a Source of Antimicrobial Peptides.

Peptide therapeutics play a key role in the development of new medical treatments. The traditional focus on endogenous peptides has shifted from first discovering other natural sources of these molecules, to later synthesizing those with unique bioactivities. This review provides concise information concerning antimicrobial peptides derived from marine crustaceans for the development of new therapeutics. Marine arthropods do not have an adaptive immune system, and therefore, they depend on the innate immune system to eliminate pathogens. In this context, antimicrobial peptides (AMPs) with unique characteristics are a pivotal part of the defense systems of these organisms. This review covers topics such as the diversity and distribution of peptides in marine arthropods (crustacea and chelicerata), with a focus on penaeid shrimps. The following aspects are covered: the defense system; classes of AMPs; molecular characteristics of AMPs; AMP synthesis; the role of penaeidins, anti-lipopolysaccharide factors, crustins, and stylicins against microorganisms; and the use of AMPs as therapeutic drugs. This review seeks to provide a useful compilation of the most recent information regarding AMPs from marine crustaceans, and describes the future potential applications of these molecules.

Chemical Conjugation in Drug Delivery Systems.

Cancer is one of the diseases with the highest mortality rate. Treatments to mitigate cancer are usually so intense and invasive that they weaken the patient to cure as dangerous as the own disease. From some time ago until today, to reduce resistance generated by the constant administration of the drug and improve its pharmacokinetics, scientists have been developing drug delivery system (DDS) technology. DDS platforms aim to maximize the drugs' effectiveness by directing them to reach the affected area by the disease and, therefore, reduce the potential side effects. Erythrocytes, antibodies, and nanoparticles have been used as carriers. Eleven antibody-drug conjugates (ADCs) involving covalent linkage has been commercialized as a promising cancer treatment in the last years. This review describes the general features and applications of DDS focused on the covalent conjugation system that binds the antibody carrier to the cytotoxic drug.

Natural Cellulose Fibers for Surgical Suture Applications.

Suture biomaterials are critical in wound repair by providing support to the healing of different tissues including vascular surgery, hemostasis, and plastic surgery. Important properties of a suture material include physical properties, handling characteristics, and biological response for successful performance. However, bacteria can bind to sutures and become a source of infection. For this reason, there is a need for new biomaterials for suture with antifouling properties. Here we report two types of cellulose fibers from coconut (Cocos nucifera) and sisal (Agave sisalana), which were purified with a chemical method, characterized, and tested in vitro and in vivo. According to SEM images, the cellulose fiber from coconut has a porous surface, and sisal has a uniform structure without internal spaces. It was found that the cellulose fiber from sisal has mechanical properties closer to silk fiber biomaterial using Ultimate Tensile Strength. When evaluating the cellulose fibers biodegradability, the cellulose from coconut showed a rapid weight loss compared to sisal. The antifouling test was negative, which demonstrated that neither possesses intrinsic microbicidal activity. Yet, a weak biofilm was formed on sisal cellulose fibers suggesting it possesses antifouling properties compared to cellulose from coconut. In vivo experiments using healthy mice demonstrated that the scarring and mechanical connection was like silk for both cellulose fibers. Overall, our results showed the potential use of cellulose fibers from vegetal for surgical sutures due to excellent mechanical properties, rapid degradation, and no bacterial adhesion.

Peptide Phage Display: Molecular Principles and Biomedical Applications.

Phage display (PD) is a technology based on the presentation of functional exogenous peptides on the capsid surface of bacteriophages. PD is performed by introducing a DNA sequence of interest at a specific position within a functional viral gene. In addition, peptide phage libraries are powerful tools for expressing a wide range of random peptides and for specific peptide screening. Specifically, PD applications include the analysis of binding and interactions between proteins, the identification of bioactive peptides that bind to receptors, the identification of disease-associated antigens, and the identification of cell-specific peptides. Since its emergence, PD technology has revolutionized several fields in the biological sciences, such as oncology, cell biology, and pharmacology, the innumerable applications for which will be described throughout this review.

Cromatografía de exclusión molecular como metodología para la purificación de bacteriófagos / Molecular exclusion chromatography as methodology for the purification of bacteriophages

La cromatografía de exclusión molecular puede ser usada para purificar fagos filamentosos, el virus bacteriano más usado en la tecnología de presentación de péptidos y proteínas en la superficie de los fagos. El bacteriófago, luego de ser precipitado del sobrenadante de cultivo con polietilenglicol, fue aplicado a una columna de Sepharose CL-4B de 100 cm de altura, usando como fase móvil solución tampón fosfato (PBS). Se obtuvo un 61,3 por ciento de recobrado del fago total aplicado y, mediante el análisis por SDS-PAGE, se verificó la pureza de estas preparaciones. La cromatografía de exclusión molecular es una metodología atractiva para la obtención de preparaciones de bacteriófagos con alta pureza(AU)

Molecular exclusion chromatography can be used to purify filamentous phages which are the most commonly used virus in phage display technology of peptides and proteins. Bacteriophages were precipitated from culture supernatant using polyethylene glycol and they were loaded in a 100 cm high CL-4B Sepharose matrix using phosphate buffer as mobile phase. We recovered 61,3percent of total phage loaded. SDS-PAGE analysis showed a high purity of these preparations. Molecular exclusion chromatography is an attractive alternative method for purifying filamentous phages(AU)

Preferential selection of Cys-constrained peptides from a random phage-displayed library by anti-glucitollysine antibodies.

Phage-displayed peptides recognized by two monoclonal antibodies against glucitollysine were selected. The most prominent feature of the peptide panel was the presence of paired Cys in most of them (21/24 peptides). The availability of a wide variety of peptides having differently spaced paired Cys, as well as truly linear Cys-free peptides, gave the opportunity to explore the role of disulfide bridges in phage selection. Some Cys-containing peptides came from a Cys-flanked cyclic 9-mer library, but most of them (18/21) were derived from a totally random 12-mer library, and hence the presence of Cys was dictated by the selector antibodies. Motifs shared by several peptides (potentially involved in binding) often contained or were flanked by Cys residues. Binding of all Cys-containing phage-displayed peptides was abolished/decreased after a reducing treatment. Screening a random peptide library (without invariant Cys residues) is powerful enough to clearly reveal the need, preferences, and diversity of Cys-mediated structural constraints for recognition.

Gangliosides, Ab1 and Ab2 antibodies I. Towards a molecular dissection of an idiotype-anti-idiotype system.

This report is focused on the molecular basis for the interaction of a monoclonal antibody (mAb) and its anti-idiotypic mAb. P3 mAb (Ab1) recognizes N-glycolyl-gangliosides, and 1E10 mAb is one of its anti-idiotypic mAbs (Ab2). Chimeric versions of both antibodies retained their specificity. Charged residues in their H-CDRs, particularly H-CDR3, were considered to play a major role in their binding and immunogenic properties. P3 mAb has the unusual property of generating a strong antibody response in syngeneic mice, even when it is administered in saline. We selected phagotopes from a 12mer peptide library displayed on filamentous phage to characterize amino acid motifs recognized by these antibodies. The peptides were enriched in charged amino acids similar to those present in P3 and 1E10 mAb H-CDR3. We also report the construction of four mutants of the P3 antibody, where arginine residues in the heavy chain CDRs were substituted by serine residues, and the characterization of their interaction with 1E10 mAb and GM3(NeuGc) ganglioside, as well as their immunogenic properties in Balb/c mice. H-CDR1 R31 residue appears to have a central role in P3 mAb reactivity and antigenicity. H-CDR3 R100a residue seems to be more involved in the immunogenicity of the P3 idiotype.

A monoclonal antibody against NeuGc-containing gangliosides contains a regulatory idiotope involved in the interaction with B and T cells.

P3 (IgM-kappa) is a monoclonal antibody (mAb) reacting with N-glycolyl neuraminic acid (NeuGc)-containing gangliosides and sulfated glycolipids. To explore the nature of the idiotope defined by 1E10, we used a phage-displayed random peptide library. After three rounds of selection, seven different phagotopes were isolated. Noteworthy, all the sequences were found to bear the basic amino acid-rich motifs KPPR (3) or RRPR/K (4). This recursive selection of basic sequences by 1E10 mAb confirmed previous suggestions of the involvement of charged residues in the interaction between gamma-type Ab2 and P3 mAb. The binding of 1E10 to phage peptides representing each group was completely inhibited by P3 mAb. In addition, other Ab2 to P3 were able to recognize these peptides. Thus, phage peptides seem to be mimotopes of the idiotope recognized by anti-idiotypic antibodies in P3. Phage motifs were represented in the lineal sequence of P3's heavy chain H-CDR3 and a 14-mer peptide representing this region was able to specifically inhibit 1E10 binding to P3. Previous studies showed that P3's idiotype was autoimmunogenic and shared by antibodies with different specificities. Now, we demonstrated that P3 mAb is able to activate a network cascade involving autologous anti-idiotypic and anti-anti-idiotypic T cells. Thus, P3's idiotype fulfill the three criteria previously established to define a "regulatory idiotype". Particularly, data presented here revealed the immunodominance of the H-CDR3 of this mAb as a T cell epitope. Thus, H-CDR3 is simultaneously involved in the interaction of P3 mAb with anti-idiotypic B and T cells, behaving as a potential regulatory idiotope.