Crytic antimicrobial peptides hidden in protein precursors: identification of novel bioactive molecules

Antibiotics are the mainstay in treatment of bacterial infections. However, resistance to antibacterial treatments has been rising since the 1970s, causing serious problems in the treatment and control of infectious diseases. Antibiotic resistance is now considered as one of the major global health threats of the 21st century in that the worldwide use of antibiotics is predicted to increase by more than 65% in the coming decades due to the increasing demand for meat and shift in agriculture practices in developing countries. New antibacterial drugs are urgently needed, but only three antibacterial drugs have been brought to the market since 1999 and very few new antibiotics are currently in development. This has prompted the search for alternatives to conventional antibiotics. Multiple alternative anti-infective strategies are being investigated, including vaccines, probiotics and phage therapy. Other promising alternatives to antibiotics are host defense peptides (HDPs), an important component of the first line of defense against infection, found in all multicellular organisms. HDPs are seen as true multifunctional peptides with activities as diverse as chemotaxis, inhibition of LPS-induced inflammation, modulation of leukocyte differentiation and promotion of wound healing. Interestingly, novel functions of these peptides are still being described to date. Many human proteins with functions not necessarily related to host defense behave as sources of HDPs. Some examples are lactoferrin, lysozyme and thrombin. Since these peptides are hidden in large proteins, they can be defined as “cryptic”. In order to identify by a rational approach further human proteins carrying cryptic HDPs, we recently developed an in-silico screening method to localize antimicrobial regions hidden inside the primary structure of precursor proteins. A wide list of potential new antimicrobial peptides was obtained by applying this method to about 4,000 human extracellular proteins. The main aim of this PhD project was the identification of interesting potential HDPs, to develop novel bioactive peptides. Firstly, we developed a novel and cost-effective method to produce recombinant HDPs, based on the use a cheap and efficient medium to be employed in an auto-inducing fermentation process. Furthermore, to avoid HDPs toxicity towards bacterial host, a novel fusion system based on a carrier protein (derived from a Rana pipiens ribonuclease) was used. Once optimized the production system, a broad characterization of two novel recombinant peptides, previously identified in human Apolipoprotein B (ApoB), was performed. We demonstrated that both peptides are endowed with a significant antimicrobial activity towards Gram-negative and Gram-positive strains, and are able to prevent biofilm formation in several strains at concentrations lower than those required to directly kill planktonic bacterial cells. Moreover, ApoB-derived peptides were found to be endowed with anti-inflammatory properties as well as the ability to promote wound healing in keratinocytes. In addition, two further cryptic HDPs have been structurally and functionally characterized. One of these HDPs has been identified in human 11-hydroxysteroid dehydrogenase-1 β-like, the other represents the first HDP from an archaeal protein, the transcription factor Stf76 encoded by the hybrid plasmid-virus pSSVx from Sulfolobus islandicus. By means of a multidisciplinary approach including biochemical, cellular biology and spectroscopic techniques, the action mechanism of both peptides has been elucidated, and intriguing results have been obtained by testing their immunomodulatory and anti-cancer activities. Hence, the in silico-derived panel of potential HDPs is a rich source of peptides with pharmacologically relevant properties

Inflammation protein quantification by multiple reaction monitoring mass spectrometry in lipopolysaccharide-stimulated THP-1 cells

Rationale: Inflammation is a cascade of events mediated by a cytokine network triggering the cellular response. In order to monitor the modulation of the crucial inflammatory proteins, e.g., Tumour Necrosis Factor-α (TNF-α), Interferon-γ (INF-γ), Interleukin-8 (IL-8) and Interleukin-10 (IL-10), upon stimulation with endotoxins, differentiated and undifferentiated THP-1 cells were treated with lipopolysaccharides (LPSs) from E. coli, key cell wall components of Gram-negative bacteria. Methods: The multiple reaction monitoring mass spectrometry (MRM-MS) method was optimized by using the standard proteins to be quantified, in order to construct external calibration curves and define the analytical parameters. The developed method was used to quantify the above-mentioned inflammatory proteins in THP-1 differentiated cells upon stimulation with LPSs with high accuracy, sensitivity, and robustness. Results: The analysis of such proteins in MRM mode allowed the kinetics of stimulation along the time up to 24 h to be followed and the MS results were found to be comparable with those obtained by Western-blotting. A significant increase in TNF-α release triggered a cascade mechanism leading to the production of INF-γ and IL-8. IL-10, instead, was found to be constant throughout the process. Conclusions: The developed MRM-MS method allowed the quantification of TNF-α, INF-γ, IL-8 and IL-10 along a time-course from 2 to 24 h. Hence, a trace of the kinetics of the inflammatory response in THP-1 cells upon stimulation with E. coli LPSs was obtained. Finally, the extensibility of the developed MRM method to serum samples and other matrices demonstrated the versatility of the approach and the possibility to quantify multiple target proteins in different biological samples by using a few microliters in a single analysis

Edible Films Made of Dried Olive Leaf Extract and Chitosan: Characterization and Applications

Nowadays a possible strategy in food preservation consists of the use of active and functional packaging to improve safety and ensure a longer shelf life of food products. Many studies refer to chitosan-based films because of the already-known chitosan (CH) antibacterial and antifungal activity. In this work, we developed CH-based films containing Dried Olive Leaf Extract (DOLE) obtained by Naviglio extractor, with the aim to investigate the polyphenols yield and the antioxidant activity of this extract entrapped in CH-based-edible films. Olive tree cultivation produces a huge amount of byproducts that are usually simply burned. Phenolic compounds are already studied for their beneficial effects on human health. Some studies reported that phenols isolated from olive leaves have been shown to inhibit the growth of different strains of microorganisms. Thus, the antimicrobial effect of DOLE-containing films against bacterial strains (Salmonella enterica subsp. enterica serovar Typhimurium ATCC® 14028, Salmonella enteritidis RIVM 706, and Enterococcus faecalis ATCC® 29212) was tested in vitro. The DOLE component of the films is effective in inhibiting all the bacteria tested in a dose-dependent manner. Thus, it was demonstrated that these edible films can act as active bioplastics when used to wrap hamburgers in substitution for baking paper, which is normally used

Cryptides Identified in Human Apolipoprotein B as New Weapons to Fight Antibiotic Resistance in Cystic Fibrosis Disease

Chronic respiratory infections are the main cause of morbidity and mortality in cystic fibrosis (CF) patients, and are characterized by the development of multidrug resistance (MDR) phenotype and biofilm formation, generally recalcitrant to treatment with conventional antibiotics. Hence, novel eective strategies are urgently needed. Antimicrobial peptides represent new promising therapeutic agents. Here, we analyze for the first time the ecacy of three versions of a cryptide identified in human apolipoprotein B (ApoB, residues 887-922) towards bacterial strains clinically isolated from CF patients. Antimicrobial and anti-biofilm properties of ApoB-derived cryptides have been analyzed by broth microdilution assays, crystal violet assays, confocal laser scanning microscopy and scanning electron microscopy. Cell proliferation assays have been performed to test cryptide eects on human host cells. ApoB-derived cryptides have been found to be endowed with significant antimicrobial and anti-biofilm properties towards Pseudomonas and Burkholderia strains clinically isolated from CF patients. Peptides have been also found to be able to act in combination with the antibiotic ciprofloxacin, and they are harmless when tested on human bronchial epithelial mesothelial cells. These findings open interesting perspectives to cryptide applicability in the treatment of chronic lung infections associated with CF disease

Host defense peptides identified in human apolipoprotein B as natural food bio-preservatives: Evaluation of their biosafety and digestibility

The employment of chemical agents in the food industry is raising several concerns by consumers and is leading to an increasing interest in natural food preservatives. Among alternatives, host defense peptides (HDPs) have attracted great interest for their ability to preserve food samples from contamination without altering their quality, taste, and organoleptic properties. Recently, we evaluated the applicability of ApoB-derived peptides as novel food bio-preservatives and demonstrated their ability to prevent chicken meat sample contamination when immobilized on chitosan films. To perform a further step towards the applicability of these peptides in the food field, here we evaluated peptides biosafety and digestibility. To do this, we used a multidisciplinary approach including the evaluation of the peptides' toxicity and antimicrobial activity, the analysis of resistance phenotype development, an in silico prediction of the peptides' susceptibility to proteases and the evaluation of the peptides' stability in simulated gastric and intestinal fluids. ApoB-derived peptides were found to be nontoxic when tested on human gastric carcinoma cells SNU-1 and on human colon-rectal adenocarcinoma cells HT-29, and not to induce resistance phenotype in Salmonella strains. Bioinformatic analyses showed that the peptides are susceptible to several proteases, as also confirmed by experiments in simulated gastric and intestinal fluids. Altogether these findings open interesting perspectives to the future applicability of ApoB-derived peptides as novel food biopreservatives

Insights into the interaction of the N-terminal amyloidogenic polypeptide of ApoA-I with model cellular membranes

BACKGROUND: About twenty variants of apolipoprotein A-I (ApoA-I) are associated to hereditary systemic amyloidoses. Although the molecular bases of this disease are still largely unknown, it has been hypothesized that ApoA-I proteolysis is a key event in pathogenesis, since it triggers the release of an N-terminal fragment (80-100 residue long) that misfolds to form amyloid deposits in peripheral organs and tissues. It is also known that cell membrane lipids play a key role in the fibrillogenic pathway. In the case of ApoA-I related amyloidosis caused by L174S mutation, the 93-residue N-terminal fragment of ApoA-I ([1-93]ApoA-I) was found to be the major constituent of ex vivo fibrils. METHODS: With the main goal to investigate the interaction of either [1-93]ApoA-I and ApoA-I with biomimetic membranes, we set-up an experimental system based on the Raman Tweezers methodology. We tested GUVs composed by two types of zwitterionic lipids with a different fluidity degree, i.e. dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC). RESULTS: We found that [1-93]ApoA-I induces conformational disorder in an ordered lipid bilayer. When interacting with fluid phases, instead, the fragment was found to be able to penetrate the membrane bilayer inducing an alignment of lipid chains. CONCLUSIONS: The interaction features of [1-93]ApoA-I with biomimetic membranes strongly depend on the lipid phase. Full-length ApoA-I was found to have similar effects, even if significantly less pronounced. GENERAL SIGNIFICANCE: Our observations shed light on still largely unknown molecular bases of ApoA-I fibrillogenic domain interaction with membranes

Novel Antimicrobial Strategies to Prevent Biofilm Infections in Catheters after Radical Cystectomy: A Pilot Study

Catheter-associated infections in bladder cancer patients, following radical cystectomy or ureterocutaneostomy, are very frequent, and the development of antibiotic resistance poses great challenges for treating biofilm-based infections. Here, we characterized bacterial communities from catheters of patients who had undergone radical cystectomy for muscle-invasive bladder cancer. We evaluated the efficacy of conventional antibiotics, alone or combined with the human ApoB-derived antimicrobial peptide r(P)ApoBLAla, to treat ureteral catheter-colonizing bacterial communities on clinically isolated bacteria. Microbial communities adhering to indwelling catheters were collected during the patients' regular catheter change schedules (28 days) and extracted within 48 h. Living bacteria were characterized using selective media and biochemical assays. Biofilm growth and novel antimicrobial strategies were analyzed using confocal laser scanning microscopy. Statistical analyses confirmed the relevance of the biofilm reduction induced by conventional antibiotics (fosfomycin, ceftriaxone, ciprofloxacin, gentamicin, and tetracycline) and a well-characterized human antimicrobial peptide r(P)ApoBLAla (1:20 ratio, respectively). Catheters showed polymicrobial communities, with Enterobactericiae and Proteus isolates predominating. In all samples, we recorded a meaningful reduction in biofilms, in both biomass and thickness, upon treatment with the antimicrobial peptide r(P)ApoBLAla in combination with low concentrations of conventional antibiotics. The results suggest that combinations of conventional antibiotics and human antimicrobial peptides might synergistically counteract biofilm growth on ureteral catheters, suggesting novel avenues for preventing catheter-associated infections in patients who have undergone radical cystectomy and ureterocutaneostomy

Synthesis, biophysical characterization and anti-HIV activity of d(TG3AG) Quadruplexes bearing hydrophobic tails at the 5'-end

Novel conjugated G-quadruplex-forming d(TG3AG) oligonucleotides, linked to hydrophobic groups through phosphodiester bonds at 50-end, have been synthesized as potential anti-HIV aptamers, via a fully automated, online phosphoramidite-based solid-phase strategy. Conjugated quadruplexes showed pronounced anti-HIV activity with some preference for HIV-1, with inhibitory activity invariably in the low micromolar range. The CD and DSC monitored thermal denaturation studies on the resulting quadruplexes, indicated the insertion of lipophilic residue at the 50-end, conferring always improved stability to the quadruplex complex (20 < DTm < 40 C). The data suggest no direct functional relationship between the thermal stability and anti-HIV activity of the folded conjugated G-quartets. It would appear that the nature of the residue at 50 end of the d(TG3AG) quadruplexes plays an important role in the thermodynamic stabilization but a minor influence on the anti-HIV activity. Moreover, a detailed CD and DSC analyses indicate a monophasic behaviour for sequences I and V, while for ODNs (II–IV) clearly show that these quadruplex structures deviate from simple two-state melting, supporting the hypothesis that intermediate states along the dissociation pathway may exis

Host defence peptides identified in human apolipoprotein B as promising antifungal agents

Therapeutic options to treat invasive fungal infections are still limited. This makes the development of novel antifungal agents highly desirable. Naturally occurring antifungal peptides represent valid candidates, since they are not harmful for human cells and are endowed with a wide range of activities and their mechanism of action is different from that of conventional antifungal drugs. Here, we characterized for the first time the antifungal properties of novel peptides identified in human apolipoprotein B. ApoB-derived peptides, here named r(P)ApoBLPro, r(P)ApoBLAla and r(P)ApoBSPro, were found to have significant fungicidal activity towards Candida albicans (C. albicans) cells. Peptides were also found to be able to slow down metabolic activity of Aspergillus niger (A. niger) spores. In addition, experiments were carried out to clarify the mechanism of fungicidal activity of ApoB-derived peptides. Peptides immediately interacted with C. albicans cell surfaces, as indicated by fluorescence live cell imaging analyses, and induced severe membrane damage, as indicated by propidium iodide uptake induced upon treatment of C. albicans cells with ApoB-derived peptides. ApoB-derived peptides were also tested on A. niger swollen spores, initial hyphae and branched mycelium. The effects of peptides were found to be more severe on swollen spores and initial hyphae compared to mycelium. Fluorescence live cell imaging analyses confirmed peptide internalization into swollen spores with a consequent accumulation into hyphae. Altogether, these findings open interesting perspectives to the application of ApoB-derived peptides as effective antifungal agents

Unveiling Molecular Recognition of Sialoglycans by Human Siglec-10

29 p.-6 fig.-2 tab.-7 fig. supl.-2 tab. supl.-1 graph. abst.Siglec-10 is an inhibitory I-type lectin selectively recognizing sialoglycans exposed on cell surfaces, involved in several patho-physiological processes. The key role Siglec-10 plays in the regulation of immune cell functions has made it a potential target for the development of immunotherapeutics against a broad range of diseases. However, the crystal structure of the protein has not been resolved for the time being and the atomic description of Siglec-10 interactions with complex glycans has not been previously unraveled. We present here the first insights of the molecular mechanisms regulating the interaction between Siglec-10 and naturally occurring sialoglycans. We used combined spectroscopic, computational and biophysical approaches to dissect glycans' epitope mapping and conformation upon binding in order to afford a description of the 3D complexes. Our outcomes provide a structural perspective for the rational design and development of high-affinity ligands to control the receptor functionality.This study was supported by the project ‘‘GLYTUNES’’ funded by MIUR Progetti di Ricerca di Rilevante Interesse Nazionale (PRIN 2017) (2017XZ2ZBK, 2019–2022) to A.S.; by progetto POR SATIN and Progetto POR CampaniaOncoterapia to A.M.; by the European Commission (H2020-MSCA- 814102-SWEET CROSSTALK project) to A.M., R.M., and A.S.. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program under grant agreement No 851356 to R.M. FSE,PON Ricerca e Innovazione 2014–2020, Azione I.1 ‘‘Dottorati Innovativi con caratterizzazione Industriale’’ is acknowledged for funding the PhD grant to R.E.F. Grants by the Spanish Ministry of Science MICINN (CTQ2017-88353-R and fellowship BES 2015–071588 to J.G.-C.) and Wellcome Trust 103744/Z/14/Z to P.R.C. are acknowledged.Peer reviewe