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Molecules for Biotechnologies

A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: closed (30 April 2019) | Viewed by 101316

Special Issue Editors

Prof. Dr. Giorgia Oliviero

E-Mail Website
Guest Editor
Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Sergio Pansini 5, 80131 Napoli, Italy
Interests: nucleoside; nucleotide and nucleic acid analogues; spectrometric and spectroscopic analysis
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Nicola Borbone

E-Mail Website
Guest Editor
Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
Interests: nucleic acid chemistry and biology; DNA quadruplexes formed by telomers, aptamers, and synthetic G-rich oligonucleotides; chemical-physical characterization of soft interfaces; hybrid interfaces; therapeutics; diagnostics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is with great pleasure that we announce the new Special Issue of Molecules, entitled “Molecules for Biotechnologies”. This Special Issue welcomes original papers and comprehensive reviews focused, but not limited, to the design, synthesis and biochemical characterization of molecules involved in biotechnological applications, such as the development of novel approaches for molecular diagnostics and biocatalysis, the obtainment of new biomaterials and drug delivery systems, the clarification of systems biology pathways or even the gene regulation. Please refer to the list of keywords for further topics.

Prof. Dr. Giorgia Oliviero
Dr. Nicola Borbone
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Synthesis
  • Oligonucleotides and analogues
  • Aptamers
  • Biosensors
  • Biocatalysis
  • Drug delivery
  • Quorum sensing
  • Medicinal chemistry
  • Peptides
  • Biomaterials

Published Papers (21 papers)

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17 pages, 2616 KiB  
Article
Thermally-Induced Lactosylation of Whey Proteins: Identification and Synthesis of Lactosylated β-lactoglobulin Epitope
by Alessandra Gasparini, Sofie Buhler, Andrea Faccini, Stefano Sforza and Tullia Tedeschi
Molecules 2020, 25(6), 1294; https://doi.org/10.3390/molecules25061294 - 12 Mar 2020
Cited by 14 | Viewed by 2864
Abstract
The high temperatures used in the production of milk may induce modifications in proteins structure. Due to occurrence of the Maillard reaction, lactose binds lysine residues in proteins, affecting the nutritional value. Milk is also an important source of allergenic proteins (i.e., caseins, [...] Read more.
The high temperatures used in the production of milk may induce modifications in proteins structure. Due to occurrence of the Maillard reaction, lactose binds lysine residues in proteins, affecting the nutritional value. Milk is also an important source of allergenic proteins (i.e., caseins, β-lactoglobulin and α-lactalbumin). Thus, this modification may also affect the allergenicity of these proteins. Focusing on milk whey proteins, a screening on different Ultra High Temperatures (UHT) and pasteurized milk samples was performed to identify lactosylation sites, in particular in protein known epitopes, and to verify the correlation between lactosylation and the harshness of the treatment. Whey proteins were extracted from milk samples after caseins precipitations at pH 4.6 and, after chymotryptic and tryptic in solution digestion, peptides were analysed by UPLC-MS and LTQ-Orbitrap. Results show the presence of lactosylated lysine residues in several known epitopes. Then, a β-lactoglobulin epitope was selected and synthesized by solid phase synthesis followed by in solution lactosylation, obtaining high reaction yields and purities. The synthesis of lactosylated allergenic epitopes, described here for the first time, is a useful tool for further studies on the technological impacts on food allergenicity. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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15 pages, 4371 KiB  
Article
Biological Characterization and Inhibition of Streptococcus pyogenes ZUH1 Causing Chronic Cystitis by Crocus sativus Methanol Extract, Bee Honey Alone or in Combination with Antibiotics: An In Vitro Study
by Seham Abdel-Shafi, Abdul-Raouf Al-Mohammadi, Sara Hamdi, Ahmed H. Moustafa and Gamal Enan
Molecules 2019, 24(16), 2903; https://doi.org/10.3390/molecules24162903 - 09 Aug 2019
Cited by 9 | Viewed by 4001
Abstract
Streptococcus pyogenes (S. pyogenes) ZUH1 was isolated and characterized using morphological, cultural and biochemical methods. The results showed that the marker genes (namely spyCEP, ssa, sic, sdaB and speG) indicating group A streptococci (GAS) were detected in the S. pyogenes genome. [...] Read more.
Streptococcus pyogenes (S. pyogenes) ZUH1 was isolated and characterized using morphological, cultural and biochemical methods. The results showed that the marker genes (namely spyCEP, ssa, sic, sdaB and speG) indicating group A streptococci (GAS) were detected in the S. pyogenes genome. The results showed that the S. pyogenes strain was inhibited by Crocus sativus methanol extract (CSME), bee honey (BH) and catfish glycoprotein (CFG). The inhibitory activity of these natural agents were compared with standard antibiotics such as Ceftazidime (30 μg/mL), Cefoperazone (75 μg/mL), Cefoxitin (30 μg/mL) and Imipenem (10 μg/mL). There was a synergistic effect between certain antibiotics and CSME. GC-MS and IR analysis of CSME showed different cyclic ketones, aldehydes, esters, alcohols and acids. The main compounds were tetradecanoic acid, safranal and isophorone. Transmission electron microscopy (TEM) images of S. pyogenes cells treated with CSME showed signs of an irregular wrinkled outer surface, fragmentation, adhesion and aggregation of damaged bacterial cells or cellular debris. The marker genes (spyCEP, ssa, sic, sdaB and speG) could be used as a rapid diagnostic tool for GAS. CSME, BH and CFG showed distinctive anti-streptococcal activity either alone or in combinations with antibiotics; their action on S. pyogenes cells was studied by TEM. There was a synergistic effect between antibiotics and Crocus sativus, bee honey, and glycoprotein against S. pyogenes ZUH1. The action of natural agents on the pathogenic cells was shown using TEM. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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17 pages, 2626 KiB  
Article
A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding
by Irene Ponzo, Friederike M. Möller, Herwin Daub and Nena Matscheko
Molecules 2019, 24(16), 2877; https://doi.org/10.3390/molecules24162877 - 08 Aug 2019
Cited by 26 | Viewed by 6091
Abstract
Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of [...] Read more.
Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer–analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We observed conformational changes induced by cations in real-time and determined the folding and unfolding kinetics of the aptamer. The aptamer’s affinity for K+ was found to be more than one order of magnitude higher than for other cations (K+ > NH4+ >> Na+ > Li+). The aptamer’s affinity to its protein target thrombin in the presence of different cations followed the same trend but differed by more than three orders of magnitude (KD = 0.15 nM to 250 nM). While the stability (kOFF) of the thrombin–TBA complex was similar in all conditions, the cation type strongly influenced the association rate (kON). These results demonstrated that protein–aptamer binding is intrinsically related to the correct aptamer fold and, hence, to the presence of stabilizing ions. Because fast binding kinetics with on-rates exceeding 108 M−1s−1 can be quantified, and folding-related phenomena can be directly resolved, switchSENSE is a useful analytical tool for in-depth characterization of aptamer–ion and aptamer–protein interactions. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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12 pages, 1557 KiB  
Communication
Design of a Human Rhinovirus-14 3C Protease-Inducible Caspase-3
by Hanna J. Wagner and Wilfried Weber
Molecules 2019, 24(10), 1945; https://doi.org/10.3390/molecules24101945 - 21 May 2019
Cited by 4 | Viewed by 4057
Abstract
The engineering of enzymes for the purpose of controlling their activity represents a valuable approach to address challenges in both fundamental and applied research. Here, we describe and compare different design strategies for the generation of a human rhinovirus-14 (HRV14) 3C protease-inducible caspase-3 [...] Read more.
The engineering of enzymes for the purpose of controlling their activity represents a valuable approach to address challenges in both fundamental and applied research. Here, we describe and compare different design strategies for the generation of a human rhinovirus-14 (HRV14) 3C protease-inducible caspase-3 (CASP3). We exemplify the application potential of the resulting protease by controlling the activity of a synthetic enzyme cascade, which represents an important motif for the design of artificial signal transduction networks. In addition, we use our engineered CASP3 to characterize the effect of aspartate mutations on enzymatic activity. Besides the identification of mutations that render the enzyme inactive, we find the CASP3-D192E mutant (aspartate-to-glutamate exchange at position 192) to be inaccessible for 3C protease-mediated cleavage. This indicates a structural change of CASP3 that goes beyond a slight misalignment of the catalytic triad. This study could inspire the design of additional engineered proteases that could be used to unravel fundamental research questions or to expand the collection of biological parts for the design of synthetic signaling pathways. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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15 pages, 1976 KiB  
Article
Characterization and Antibacterial Activity of 7S and 11S Globulins Isolated from Cowpea Seed Protein
by Seham Abdel-Shafi, Abdul-Raouf Al-Mohammadi, Ali Osman, Gamal Enan, Samar Abdel-Hameid and Mahmoud Sitohy
Molecules 2019, 24(6), 1082; https://doi.org/10.3390/molecules24061082 - 19 Mar 2019
Cited by 51 | Viewed by 3892
Abstract
The present work was carried out to determine the characteristics and antibacterial activity of 7S and 11S globulins isolated from cowpea seed (Vigna unguiculata (L.) Walp.). The molecular mass of 7S globulin was demonstrated by SDS-PAGE bands to be of about 132, [...] Read more.
The present work was carried out to determine the characteristics and antibacterial activity of 7S and 11S globulins isolated from cowpea seed (Vigna unguiculata (L.) Walp.). The molecular mass of 7S globulin was demonstrated by SDS-PAGE bands to be of about 132, 129 and 95 kDa corresponding the α/, α and β subunits. The molecular mass of 11S globulin was demonstrated by SDS-PAGE bands to be existed between 28 and 52 kDa corresponding the basic and acidic subunits. The minimum inhibitory concentrations MICs of 7S and 11S globulins isolated from cowpea seed were determined against Gram positive bacteria viz: Listeria monocytogenes LMG 10470, Listeria ivanovii FLB 12, Staphylococcus aureus ATCC 25923 and Streptococcus pyogenes ATCC 19615, and Gram negative bacteria such as Klebsiella pneumonia ATCC 43816, Pseudomonas aeruginosa ATCC 26853, Escherichia coli ATCC 25922 and Salmonella ATCC 14028 using disc diffusion assay; they were showed to be in the range 10 to 200 µg/mL. Transmission electron microscope (TEM) examination of the protein-treated bacteria showed the antibacterial action of 11S globulin against S. typhimurium and P. aeruginosa was manifested by signs of cellular deformation, partial and complete lysis of cell components. Adding 11S globulin at both concentrations 50 and 100 µg/g to minced meat showed considerable decreases in bacterial counts of viable bacteria, psychrotrophs and coliforms compared to controls during 15 days storage at 4 °C, reflecting a promising perspective to use such globulin as a meat bio-preservative. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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14 pages, 2008 KiB  
Article
Introduction of Nonacidic Side Chains on 6-Ethylcholane Scaffolds in the Identification of Potent Bile Acid Receptor Agonists with Improved Pharmacokinetic Properties
by Claudia Finamore, Giuliana Baronissi, Silvia Marchianò, Francesco Saverio Di Leva, Adriana Carino, Maria Chiara Monti, Vittorio Limongelli, Angela Zampella, Stefano Fiorucci and Valentina Sepe
Molecules 2019, 24(6), 1043; https://doi.org/10.3390/molecules24061043 - 16 Mar 2019
Cited by 3 | Viewed by 2781
Abstract
As a cellular bile acid sensor, farnesoid X receptor (FXR) and the membrane G-coupled receptor (GPBAR1) participate in maintaining bile acid, lipid, and glucose homeostasis. To date, several selective and dual agonists have been developed as promising pharmacological approach to metabolic disorders, with [...] Read more.
As a cellular bile acid sensor, farnesoid X receptor (FXR) and the membrane G-coupled receptor (GPBAR1) participate in maintaining bile acid, lipid, and glucose homeostasis. To date, several selective and dual agonists have been developed as promising pharmacological approach to metabolic disorders, with most of them possessing an acidic conjugable function that might compromise their pharmacokinetic distribution. Here, guided by docking calculations, nonacidic 6-ethyl cholane derivatives have been prepared. In vitro pharmacological characterization resulted in the identification of bile acid receptor modulators with improved pharmacokinetic properties. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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28 pages, 4440 KiB  
Article
Simultaneous Quantification of L-Arginine and Monosaccharides during Fermentation: An Advanced Chromatography Approach
by Mireille Ginésy, Josefine Enman, Daniela Rusanova-Naydenova and Ulrika Rova
Molecules 2019, 24(4), 802; https://doi.org/10.3390/molecules24040802 - 22 Feb 2019
Cited by 5 | Viewed by 4817
Abstract
Increasing demand for L-arginine by the food and pharmaceutical industries has sparked the search for sustainable ways of producing it. Microbial fermentation offers a suitable alternative; however, monitoring of arginine production and carbon source uptake during fermentation, requires simple and reliable quantitative methods [...] Read more.
Increasing demand for L-arginine by the food and pharmaceutical industries has sparked the search for sustainable ways of producing it. Microbial fermentation offers a suitable alternative; however, monitoring of arginine production and carbon source uptake during fermentation, requires simple and reliable quantitative methods compatible with the fermentation medium. Two methods for the simultaneous quantification of arginine and glucose or xylose are described here: high-performance anion-exchange chromatography coupled to integrated pulsed amperometric detection (HPAEC-IPAD) and reversed-phase ultra-high-performance liquid chromatography combined with charged aerosol detection (RP-UHPLC-CAD). Both were thoroughly validated in a lysogeny broth, a minimal medium, and a complex medium containing corn steep liquor. HPAEC-IPAD displayed an excellent specificity, accuracy, and precision for arginine, glucose, and xylose in minimal medium and lysogeny broth, whereas specificity and accuracy for arginine were somewhat lower in medium containing corn steep liquor. RP-UHPLC-CAD exhibited high accuracy and precision, and enabled successful monitoring of arginine and glucose or xylose in all media. The present study describes the first successful application of the above chromatographic methods for the determination and monitoring of L-arginine amounts during its fermentative production by a genetically modified Escherichia coli strain cultivated in various growth media. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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11 pages, 1314 KiB  
Article
Lateral Flow Aptasensor for Simultaneous Detection of Platelet-Derived Growth Factor-BB (PDGF-BB) and Thrombin
by Guodong Liu, Anant S Gurung and Wanwei Qiu
Molecules 2019, 24(4), 756; https://doi.org/10.3390/molecules24040756 - 20 Feb 2019
Cited by 22 | Viewed by 5130
Abstract
Here we report a lateral flow aptasensor (LFA) for the simultaneous detection of platelet-derived growth factor-BB (PDGF-BB) and thrombin. Two pairs of aptamers, which are specific against PDGF-BB and thrombin, respectively, were used to prepare the LFA. Thiolated aptamers were immobilized on a [...] Read more.
Here we report a lateral flow aptasensor (LFA) for the simultaneous detection of platelet-derived growth factor-BB (PDGF-BB) and thrombin. Two pairs of aptamers, which are specific against PDGF-BB and thrombin, respectively, were used to prepare the LFA. Thiolated aptamers were immobilized on a gold nanoparticle (AuNP) surface and biotinylated aptamers were immobilized on the test zones of an LFA nitrocellulose membrane. The assay involved the capture of PDGF-BB and thrombin simultaneously in sandwich-type formats between the capture aptamers on the test zones of LFA and AuNP-labeled detection aptamers. AuNPs were thus captured on the test zones of the LFA and gave red bands to enable the visual detection of target proteins. Quantitative results were obtained by reading the test band intensities with a portable strip reader. By combining the highly specific molecular recognition properties of aptamers with the unique properties of lateral flow assay (low-cost, short assay time and a user-friendly format), the optimized aptasensor was capable of simultaneously detecting 1.0 nM of PDGF-BB and 1.5 nM of thrombin in association with a 10-min assay time. The biosensor was also successfully applied to detect PDGF-BB and thrombin in spiked human serum samples. The LFA shows great promise for the development of aptamer-based lateral flow strip biosensors for point-of-care or for the in-field detection of disease-related protein biomarkers. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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15 pages, 3159 KiB  
Article
New G-Quadruplex-Forming Oligodeoxynucleotides Incorporating a Bifunctional Double-Ended Linker (DEL): Effects of DEL Size and ODNs Orientation on the Topology, Stability, and Molecularity of DEL-G-Quadruplexes
by Maria Marzano, Andrea Patrizia Falanga, Stefano D’Errico, Brunella Pinto, Giovanni Nicola Roviello, Gennaro Piccialli, Giorgia Oliviero and Nicola Borbone
Molecules 2019, 24(3), 654; https://doi.org/10.3390/molecules24030654 - 12 Feb 2019
Cited by 7 | Viewed by 3899
Abstract
G-quadruplexes (G4s) are unusual secondary structures of DNA occurring in guanosine-rich oligodeoxynucleotide (ODN) strands that are extensively studied for their relevance to the biological processes in which they are involved. In this study, we report the synthesis of a new kind of G4-forming [...] Read more.
G-quadruplexes (G4s) are unusual secondary structures of DNA occurring in guanosine-rich oligodeoxynucleotide (ODN) strands that are extensively studied for their relevance to the biological processes in which they are involved. In this study, we report the synthesis of a new kind of G4-forming molecule named double-ended-linker ODN (DEL-ODN), in which two TG4T strands are attached to the two ends of symmetric, non-nucleotide linkers. Four DEL-ODNs differing for the incorporation of either a short or long linker and the directionality of the TG4T strands were synthesized, and their ability to form G4 structures and/or multimeric species was investigated by PAGE, HPLC–size-exclusion chromatography (HPLC–SEC), circular dichroism (CD), and NMR studies in comparison with the previously reported monomeric tetra-ended-linker (TEL) analogues and with the corresponding tetramolecular species (TG4T)4. The structural characterization of DEL-ODNs confirmed the formation of stable, bimolecular DEL-G4s for all DEL-ODNs, as well as of additional DEL-G4 multimers with higher molecular weights, thus suggesting a way towards the obtainment of thermally stable DNA nanostructures based on reticulated DEL-G4s. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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12 pages, 3459 KiB  
Article
Gelatin-Based Hydrogels through Homobifunctional Triazolinediones Targeting Tyrosine Residues
by Roberto Guizzardi, Luca Vaghi, Marcello Marelli, Antonino Natalello, Ivan Andreosso, Antonio Papagni and Laura Cipolla
Molecules 2019, 24(3), 589; https://doi.org/10.3390/molecules24030589 - 07 Feb 2019
Cited by 14 | Viewed by 4819
Abstract
Gelatin is a biopolymer with interesting properties that can be useful for biomaterial design for different applications such as drug delivery systems, or 3D scaffolds for tissue engineering. However, gelatin suffers from poor mechanical stability at physiological temperature, hence methods for improving its [...] Read more.
Gelatin is a biopolymer with interesting properties that can be useful for biomaterial design for different applications such as drug delivery systems, or 3D scaffolds for tissue engineering. However, gelatin suffers from poor mechanical stability at physiological temperature, hence methods for improving its properties are highly desirable. In the present work, a new chemical cross-linking strategy based on triazolinedione ene-type chemistry towards stable hydrogel is proposed. Two different homobifunctional 1,2,4-triazoline-3,5(4H)-diones, namely 4,4′-hexane-1,6-diylbis(3H-1,2,4-triazoline-3,5(4H)-dione) 1 and 4,4′-[methylenebis(4,1-phenylene)]bis(3H-1,2,4-triazoline-3,5(4H)-dione) 2 were used as cross-linkers in different ratio to tyrosine residues in gelatin. The reaction was proved effective in all experimented conditions and hydrogels featured with different thermal stability were obtained. In general, the higher the cross-linker/tyrosine ratio, the more thermostable the hydrogel. The swelling properties are strictly dependent upon the chemical nature of the cross-linker. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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11 pages, 2433 KiB  
Article
Chiral Recognition of L- and D- Amino Acid by Porphyrin Supramolecular Aggregates
by Rosalba Randazzo, Massimiliano Gaeta, Chiara Maria Antonietta Gangemi, Maria Elena Fragalà, Roberto Purrello and Alessandro D’Urso
Molecules 2019, 24(1), 84; https://doi.org/10.3390/molecules24010084 - 27 Dec 2018
Cited by 32 | Viewed by 5200
Abstract
We report of the interactions between four amino acids lysine (Lys), arginine (Arg), histidine (His), and phenylalanine (Phe) with the J-aggregates of the protonated 5,10,15,20-tetrakis(4-sulfonatophenyl)-porphyrin H4TPPS. Several aspects of these self-assembled systems have been analyzed: (i) the chiral transfer process; (ii) [...] Read more.
We report of the interactions between four amino acids lysine (Lys), arginine (Arg), histidine (His), and phenylalanine (Phe) with the J-aggregates of the protonated 5,10,15,20-tetrakis(4-sulfonatophenyl)-porphyrin H4TPPS. Several aspects of these self-assembled systems have been analyzed: (i) the chiral transfer process; (ii) the hierarchical effects leading to the aggregates formation; and, (iii) the influence of the amino acid concentrations on both transferring and storing chiral information. We have demonstrated that the efficient control on the J-aggregates chirality is obtained when all amino acids are tested and that the chirality transfer process is under hierarchical control. Finally, the chiral porphyrin aggregates obtained exhibit strong chiral inertia. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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15 pages, 2754 KiB  
Article
Converting Galactose into the Rare Sugar Talose with Cellobiose 2-Epimerase as Biocatalyst
by Stevie Van Overtveldt, Ophelia Gevaert, Martijn Cherlet, Koen Beerens and Tom Desmet
Molecules 2018, 23(10), 2519; https://doi.org/10.3390/molecules23102519 - 01 Oct 2018
Cited by 15 | Viewed by 4931
Abstract
Cellobiose 2-epimerase from Rhodothermus marinus (RmCE) reversibly converts a glucose residue to a mannose residue at the reducing end of β-1,4-linked oligosaccharides. In this study, the monosaccharide specificity of RmCE has been mapped and the synthesis of d-talose from [...] Read more.
Cellobiose 2-epimerase from Rhodothermus marinus (RmCE) reversibly converts a glucose residue to a mannose residue at the reducing end of β-1,4-linked oligosaccharides. In this study, the monosaccharide specificity of RmCE has been mapped and the synthesis of d-talose from d-galactose was discovered, a reaction not yet known to occur in nature. Moreover, the conversion is industrially relevant, as talose and its derivatives have been reported to possess important antimicrobial and anti-inflammatory properties. As the enzyme also catalyzes the keto-aldo isomerization of galactose to tagatose as a minor side reaction, the purity of talose was found to decrease over time. After process optimization, 23 g/L of talose could be obtained with a product purity of 86% and a yield of 8.5% (starting from 4 g (24 mmol) of galactose). However, higher purities and concentrations can be reached by decreasing and increasing the reaction time, respectively. In addition, two engineering attempts have also been performed. First, a mutant library of RmCE was created to try and increase the activity on monosaccharide substrates. Next, two residues from RmCE were introduced in the cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) (S99M/Q371F), increasing the kcat twofold. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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10 pages, 3059 KiB  
Article
A Phytochemical-Based Copolymer Derived from Coriolus versicolor Polysaccharopeptides for Gene Delivery
by Wing-Fu Lai, Marie C. Lin and Guping Tang
Molecules 2018, 23(9), 2273; https://doi.org/10.3390/molecules23092273 - 06 Sep 2018
Cited by 3 | Viewed by 3230
Abstract
Coriolus versicolor is an herb widely used for cancer treatment in traditional Chinese medicine. Its active ingredients, polysaccharopeptides (PSP), have been used for adjuvant therapies in cancer treatment. This study conjugates Coriolus versicolor PSP with poly(ethylenimine) (PEI) to generate a PSP-PEI copolymer for [...] Read more.
Coriolus versicolor is an herb widely used for cancer treatment in traditional Chinese medicine. Its active ingredients, polysaccharopeptides (PSP), have been used for adjuvant therapies in cancer treatment. This study conjugates Coriolus versicolor PSP with poly(ethylenimine) (PEI) to generate a PSP-PEI copolymer for gene transfer. After PEI conjugation, both the pH buffering capacity and DNA compaction ability of PSP are significantly increased. Compared with that of PSP, the transfection efficiency of PSP-PEI is 10 to 20-fold higher in vitro. This is a proof-of-concept study reporting the direct use of bioactive phytochemicals from traditional Chinese medicine for gene vector development. The promising performance of PSP-PEI raises the possibility that bioactive herbal ingredients can be further developed as a multi-therapeutic gene carrier for tackling cancers. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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12 pages, 1819 KiB  
Article
Spectroscopic Characterization of Natural Melanin from a Streptomyces cyaneofuscatus Strain and Comparison with Melanin Enzymatically Synthesized by Tyrosinase and Laccase
by Maher Al Khatib, Mohamed Harir, Jessica Costa, Maria Camilla Baratto, Irene Schiavo, Lorenza Trabalzini, Simona Pollini, Gian Maria Rossolini, Riccardo Basosi and Rebecca Pogni
Molecules 2018, 23(8), 1916; https://doi.org/10.3390/molecules23081916 - 01 Aug 2018
Cited by 31 | Viewed by 5908
Abstract
An actinobacteria strain was isolated from Algerian Sahara soil and assigned to Streptomyces cyaneofuscatus Pridham et al. 1958 species. This strain was selected for its ability to produce melanin exopigments in liquid and solid media. Melanin synthesis was associated with tyrosinase activity and [...] Read more.
An actinobacteria strain was isolated from Algerian Sahara soil and assigned to Streptomyces cyaneofuscatus Pridham et al. 1958 species. This strain was selected for its ability to produce melanin exopigments in liquid and solid media. Melanin synthesis was associated with tyrosinase activity and the enzyme from this strain was isolated and biochemically characterized. Synthetic melanin was then enzymatically produced using the S. cyaneofuscatus Pridham et al. 1958 tyrosinase. As this enzyme showed a higher diphenolase activity, a synthetic melanin from the enzymic oxidation of 3,4-dihydroxyphenylalanine (dopa) was obtained by the use of a Trametes versicolor (L.) Lloyd laccase for comparison. The natural and synthetic pigments were physico-chemically characterized by the use of ultraviolet (UV)-Visible, and Fourier transform infrared (FT-IR) and multifrequency electron paramagnetic resonance (EPR) spectroscopies. All the melanin samples displayed a stable free radical when analyzed by X-band EPR spectroscopy. Once the samples were recorded at Q-band EPR, a copolymer derived from a mixture of different constituents was evident in the natural melanin. All radical species were analyzed and discussed. The use of water-soluble melanin naturally produced by S. cyaneofuscatus Pridham et al. 1958 represents a new biotechnological alternative to commercial insoluble pigments. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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17 pages, 3259 KiB  
Article
Design, Synthesis and Characterization of Novel Co-Polymers Decorated with Peptides for the Selective Nanoparticle Transport across the Cerebral Endothelium
by Andrea P. Falanga, Pietro Melone, Roberta Cagliani, Nicola Borbone, Stefano D’Errico, Gennaro Piccialli, Paolo A. Netti and Daniela Guarnieri
Molecules 2018, 23(7), 1655; https://doi.org/10.3390/molecules23071655 - 06 Jul 2018
Cited by 19 | Viewed by 4123
Abstract
The development of new strategies for enhancing drug delivery to the brain represents a major challenge in treating cerebral diseases. In this paper, we report on the synthesis and structural characterization of a biocompatible nanoparticle (NP) made up of poly(lactic-co-glycolic acid) (PLGA)-polyethylene glycol [...] Read more.
The development of new strategies for enhancing drug delivery to the brain represents a major challenge in treating cerebral diseases. In this paper, we report on the synthesis and structural characterization of a biocompatible nanoparticle (NP) made up of poly(lactic-co-glycolic acid) (PLGA)-polyethylene glycol (PEG) co-polymer (namely PELGA) functionalized with the membranotropic peptide gH625 (gH) and the iron-mimicking peptide CRTIGPSVC (CRT) for transport across the blood-brain barrier (BBB). gH possesses a high translocation potency of the cell membrane. Conversely, CRT selectively recognizes the brain endothelium, which interacts with transferrin (Tf) and its receptor (TfR) through a non-canonical ligand-directed mechanism. We hypothesize that the delivery across the BBB of PELGA NPs should be efficiently enhanced by the NP functionalization with both gH and CRT. Synthesis of peptides and their conjugation to the PLGA as well as NP physical-chemical characterization are performed. Moreover, NP uptake, co-localization, adhesion under dynamic conditions, and permeation across in vitro BBB model are evaluated as a function of gH/CRT functionalization ratio. Results establish that the cooperative effect of CRT and gH may change the intra-cellular distribution of NPs and strengthen NP delivery across the BBB at the functionalization ratio 33% gH–66% CRT. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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10 pages, 1416 KiB  
Article
Lipase Catalysed Kinetic Resolution of Racemic 1,2-Diols Containing a Chiral Quaternary Center
by Gonzalo De Gonzalo
Molecules 2018, 23(7), 1585; https://doi.org/10.3390/molecules23071585 - 29 Jun 2018
Cited by 3 | Viewed by 3901 | Correction
Abstract
Optically active 1,2-diols are valuable buildings blocks in organic synthesis. In the present paper, a set of racemic 1,2-diols with an ester functional group are prepared, starting from α-ketoesters in a three-step procedure with moderate yields. The racemic 1,2-diols, containing a chiral quaternary [...] Read more.
Optically active 1,2-diols are valuable buildings blocks in organic synthesis. In the present paper, a set of racemic 1,2-diols with an ester functional group are prepared, starting from α-ketoesters in a three-step procedure with moderate yields. The racemic 1,2-diols, containing a chiral quaternary center in their structure, are subjected to selective acylation in order to perform their kinetic resolution catalysed by a set of commercially available lipases. Under optimized reaction conditions, good conversions and enantioselectivities are achieved by using the lipase PSL-C from Pseudomonas cepacia in tert-butyl methyl ether. This biocatalyst could be reused up to five times without losing its properties. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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10 pages, 5477 KiB  
Article
A Highly Selective and Strong Anti-Interference Host-Guest Complex as Fluorescent Probe for Detection of Amantadine by Indicator Displacement Assay
by Linzhao Zhu, Zhiyong Zhao, Xiongzhi Zhang, Haijun Zhang, Feng Liang and Simin Liu
Molecules 2018, 23(4), 947; https://doi.org/10.3390/molecules23040947 - 18 Apr 2018
Cited by 14 | Viewed by 4075
Abstract
Amantadine (AMA) and its derivatives are illicit veterinary drugs that are hard to detect at very low concentrations. Developing a fast, simple and highly sensitive method for the detection of AMA is highly in demand. Here, we designed an anthracyclic compound (ABAM) that [...] Read more.
Amantadine (AMA) and its derivatives are illicit veterinary drugs that are hard to detect at very low concentrations. Developing a fast, simple and highly sensitive method for the detection of AMA is highly in demand. Here, we designed an anthracyclic compound (ABAM) that binds to a cucurbit[7]uril (CB[7]) host with a high association constant of up to 8.7 × 108 M−1. The host-guest complex was then used as a fluorescent probe for the detection of AMA. Competition by AMA for occupying the cavity of CB[7] allows ABAM to release from the CB[7]-ABAM complex, causing significant fluorescence quenching of ABAM (indicator displacement assay, IDA). The linear range of the method is from 0.000188 to 0.375 μg/mL, and the detection limit can be as low as 6.5 × 10−5 μg/mL (0.35 nM). Most importantly, due to the high binding affinity between CB[7] and ABAM, this fluorescence host-guest system shows great anti-interference capacity. Thus, we are able to accurately determine the concentration of AMA in various samples, including pharmaceutical formulations. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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Review

Jump to: Research, Other

14 pages, 3051 KiB  
Review
Porous Silicon-Based Aptasensors: The Next Generation of Label-Free Devices for Health Monitoring
by Monica Terracciano, Ilaria Rea, Nicola Borbone, Rosalba Moretta, Giorgia Oliviero, Gennaro Piccialli and Luca De Stefano
Molecules 2019, 24(12), 2216; https://doi.org/10.3390/molecules24122216 - 13 Jun 2019
Cited by 23 | Viewed by 3574
Abstract
Aptamers are artificial nucleic acid ligands identified and obtained from combinatorial libraries of synthetic nucleic acids through the in vitro process SELEX (systematic evolution of ligands by exponential enrichment). Aptamers are able to bind an ample range of non-nucleic acid targets with great [...] Read more.
Aptamers are artificial nucleic acid ligands identified and obtained from combinatorial libraries of synthetic nucleic acids through the in vitro process SELEX (systematic evolution of ligands by exponential enrichment). Aptamers are able to bind an ample range of non-nucleic acid targets with great specificity and affinity. Devices based on aptamers as bio-recognition elements open up a new generation of biosensors called aptasensors. This review focuses on some recent achievements in the design of advanced label-free optical aptasensors using porous silicon (PSi) as a transducer surface for the detection of pathogenic microorganisms and diagnostic molecules with high sensitivity, reliability and low limit of detection (LoD). Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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16 pages, 3088 KiB  
Review
Optical Biosensors Based on Silicon-On-Insulator Ring Resonators: A Review
by Patrick Steglich, Marcel Hülsemann, Birgit Dietzel and Andreas Mai
Molecules 2019, 24(3), 519; https://doi.org/10.3390/molecules24030519 - 31 Jan 2019
Cited by 139 | Viewed by 8887
Abstract
Recent developments in optical biosensors based on integrated photonic devices are reviewed with a special emphasis on silicon-on-insulator ring resonators. The review is mainly devoted to the following aspects: (1) Principles of sensing mechanism, (2) sensor design, (3) biofunctionalization procedures for specific molecule [...] Read more.
Recent developments in optical biosensors based on integrated photonic devices are reviewed with a special emphasis on silicon-on-insulator ring resonators. The review is mainly devoted to the following aspects: (1) Principles of sensing mechanism, (2) sensor design, (3) biofunctionalization procedures for specific molecule detection and (4) system integration and measurement set-ups. The inherent challenges of implementing photonics-based biosensors to meet specific requirements of applications in medicine, food analysis, and environmental monitoring are discussed. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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27 pages, 2288 KiB  
Review
Peptide-Based Drug-Delivery Systems in Biotechnological Applications: Recent Advances and Perspectives
by Diego Tesauro, Antonella Accardo, Carlo Diaferia, Vittoria Milano, Jean Guillon, Luisa Ronga and Filomena Rossi
Molecules 2019, 24(2), 351; https://doi.org/10.3390/molecules24020351 - 19 Jan 2019
Cited by 168 | Viewed by 11791
Abstract
Peptides of natural and synthetic sources are compounds operating in a wide range of biological interactions. They play a key role in biotechnological applications as both therapeutic and diagnostic tools. They are easily synthesized thanks to solid-phase peptide devices where the amino acid [...] Read more.
Peptides of natural and synthetic sources are compounds operating in a wide range of biological interactions. They play a key role in biotechnological applications as both therapeutic and diagnostic tools. They are easily synthesized thanks to solid-phase peptide devices where the amino acid sequence can be exactly selected at molecular levels, by tuning the basic units. Recently, peptides achieved resounding success in drug delivery and in nanomedicine smart applications. These applications are the most significant challenge of recent decades: they can selectively deliver drugs to only pathological tissues whilst saving the other districts of the body. This specific feature allows a reduction in the drug side effects and increases the drug efficacy. In this context, peptide-based aggregates present many advantages, including biocompatibility, high drug loading capacities, chemical diversity, specific targeting, and stimuli responsive drug delivery. A dual behavior is observed: on the one hand they can fulfill a structural and bioactive role. In this review, we focus on the design and the characterization of drug delivery systems using peptide-based carriers; moreover, we will also highlight the peptide ability to self-assemble and to actively address nanosystems toward specific targets. Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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Other

Jump to: Research, Review

2 pages, 867 KiB  
Correction
Correction: de Gonzalo, G. Lipase Catalysed Kinetic Resolution of Racemic 1,2-Diols Containing a Chiral Quaternary Center. Molecules 2018, 23, 1585
by Gonzalo De Gonzalo
Molecules 2018, 23(10), 2503; https://doi.org/10.3390/molecules23102503 - 29 Sep 2018
Cited by 1 | Viewed by 1979
Abstract
The authors wish to make the following corrections to their paper. [...] Full article
(This article belongs to the Special Issue Molecules for Biotechnologies)
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