Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking

• Kendra Ramirez-Acosta,
• Ivan A. Rosales-Fuerte,
• J. Eduardo Perez-Sanchez,
• Alfredo Nuñez-Rivera,
• Josue Juarez and
• Ruben D. Cadena-Nava

Beilstein J. Nanotechnol. 2022, 13, 699–711, doi:10.3762/bjnano.13.62

• , peptides with great affinity to the RBD were selected. The most common amino acids involved in the recognition of the RBD were identified to design novel peptides based on the number of hydrogen bonds that were formed. At physiological pH, these peptides are almost neutral and soluble in aqueous media

• temporin B and lysozyme (61–80). The net charge calculated for the OAPs varies according to the number of negatively and positively charged amino acids present in the primary structure. The net charge values are in the range of −3.9 to 2.9 at pH 7. The OAPs were selected based on an absolute value of the

• been reported by Debmalya and co-workers, who analyzed the potential of chimeric peptides to block the RBD using an in silico approach. They found that a peptide with 26 amino acids binds to the Thr500 and Asn501 residues of the RBD, while a peptide with 23 amino acids binds to the Tyr489 and Thr500

Stimuli-responsive polypeptide nanogels for trypsin inhibition

• Petr Šálek,
• Jana Dvořáková,
• Sviatoslav Hladysh,
• Diana Oleshchuk,
• Ewa Pavlova,
• Jan Kučka and
• Vladimír Proks

Beilstein J. Nanotechnol. 2022, 13, 538–548, doi:10.3762/bjnano.13.45

• trypsin because they contain suitable amino acids in their structures that effectively block the active site of trypsin. Keywords: α1-antitrypsin; inflammatory mediator; nanogel; polypeptide; trypsin; Introduction Despite significant and progressive advances in medicine, the global incidence of

• , have the ability to inhibit the trypsin active site because they contain positively charged amino acids (containing NH2 terminal groups) and aromatic amino acids [23][25]. It is known that inhibitors containing these amino acids in their structure can block the active site of trypsin because they

Self-assembly of amino acids toward functional biomaterials

• Huan Ren,
• Lifang Wu,
• Lina Tan,
• Yanni Bao,
• Yuchen Ma,
• Yong Jin and
• Qianli Zou

Beilstein J. Nanotechnol. 2021, 12, 1140–1150, doi:10.3762/bjnano.12.85

• nanostructures at both microscopic and macroscopic scales. Amino acids, as the smallest constituent of proteins and the smallest constituent in the bottom-up approach, are the smallest building blocks that can be self-assembled. The self-assembly of single amino acids has the advantages of low synthesis cost

• , simple modeling, excellent biocompatibility and biodegradability in vivo. In addition, amino acids can be assembled with other components to meet multiple scientific needs. However, using these simple building blocks to design attractive materials remains a challenge due to the simplicity of the amino

• acids. Most of the review articles about self-assembly focus on large molecules, such as peptides and proteins. The preparation of complicated materials by self-assembly of amino acids has not yet been evaluated. Therefore, it is of great significance to systematically summarize the literature of amino

pH-driven enhancement of anti-tubercular drug loading on iron oxide nanoparticles for drug delivery in macrophages

• Karishma Berta Cotta,
• Sarika Mehra and
• Rajdip Bandyopadhyaya

Beilstein J. Nanotechnol. 2021, 12, 1127–1139, doi:10.3762/bjnano.12.84

• acid with fluorine and a piperazine ring [25]. It exhibits a zwitterionic nature, with a pKa1 and pKa2 of 6.2 and 8.5, respectively [26]. Zwitterionic molecules like amino acids and amphoteric hydroxy groups get adsorbed onto iron oxide nanoparticles predominately via electrostatic interaction [27][28

• ]. Furthermore, their interaction with IONPs may be via carboxylate groups, amine groups or by neither [27]. pH variations thus can play a key role in promoting interactions between amino acids and metal oxide surfaces [29]. NOR has also been reported to form stable complexes with Fe2+/3+ [22]. It was also

The role of deep eutectic solvents and carrageenan in synthesizing biocompatible anisotropic metal nanoparticles

• Nabojit Das,
• Akash Kumar and
• Raja Gopal Rayavarapu

Beilstein J. Nanotechnol. 2021, 12, 924–938, doi:10.3762/bjnano.12.69

• for dissolving many species of high polarity, for example, amino acids, metal salts, glycerol, benzoic acid, citric acid, and glucose [26][76]. They are also promising in the dissolution of different polymers, such as starch, cellulose, lignin, chitin, and are also used in the pre-treatment of

Straightforward synthesis of gold nanoparticles by adding water to an engineered small dendrimer

• Sébastien Gottis,
• Régis Laurent,
• Vincent Collière and
• Anne-Marie Caminade

Beilstein J. Nanotechnol. 2020, 11, 1110–1118, doi:10.3762/bjnano.11.95

• amino acids such as ʟ-histidine, which have been used to synthesize gold nanoparticles at a higher temperature (80 °C) [49], or cysteine [50]. The compound 1 was the dendrimer chosen for the functionalization with the Girard’s T reagent. The synthesis was performed via the Staudinger reaction between

A 3D-polyphenylalanine network inside porous alumina: Synthesis and characterization of an inorganic–organic composite membrane

• Jonathan Stott and
• Jörg J. Schneider

Beilstein J. Nanotechnol. 2020, 11, 938–951, doi:10.3762/bjnano.11.78

• spectroscopic analysis provides qualitative information of the secondary structure of the grafted poly(amino acids). The measurement of the water contact angle allows conclusions regarding the hydrophobic or hydrophilic properties of the functionalized surface as well as the microstructure of the grafted

• filter holder from Millipore and sealed with silicone rings. Hydrolysis of methoxy groups and functionalization of the surface of the ALOX-membrane due a condensation reaction between hydroxyl groups on the surface and hydroxylated silanes. Synthesis of NCA-monomers from α-amino acids and triphosgene

Key for crossing the BBB with nanoparticles: the rational design

• Sonia M. Lombardo,
• Marc Schneider,
• Akif E. Türeli and
• Nazende Günday Türeli

Beilstein J. Nanotechnol. 2020, 11, 866–883, doi:10.3762/bjnano.11.72

• the brain of specific molecules such as nutrients or amino acids, transport proteins are present on the luminal and basolateral side of the endothelial cells. For instance, GLUT-1, large neutral amino acid transporters (LAT), nucleoside transporters and also organic cation and anion transporters have

• crossing through AMT by increasing the positive charge on the nanoparticle surface [125]. Another investigated way to increase BBB permeation is to use cell-penetrating peptides (CPPs). These peptides usually contain between five and 40 amino acids, including a large amount of basic amino-acid residues

Preparation and in vivo evaluation of glyco-gold nanoparticles carrying synthetic mycobacterial hexaarabinofuranoside

• Gennady L. Burygin,
• Polina I. Abronina,
• Nikita M. Podvalnyy,
• Sergey A. Staroverov,
• Leonid O. Kononov and
• Lev A. Dykman

Beilstein J. Nanotechnol. 2020, 11, 480–493, doi:10.3762/bjnano.11.39

• yet. Indeed, the direct conjugation of amino-functionalized antigenic glycans with pre-formed GNPs has not been reported yet, to the best of our knowledge. This is despite the fact that simple amines, amino acids and peptides [68][69][70][71][72][73][74][75][76][77][78], as well as diethylaminoethyl

Brome mosaic virus-like particles as siRNA nanocarriers for biomedical purposes

• Alfredo Nuñez-Rivera,
• Pierrick G. J. Fournier,
• Danna L. Arellano,
• Ana G. Rodriguez-Hernandez,
• Rafael Vazquez-Duhalt and
• Ruben D. Cadena-Nava

Beilstein J. Nanotechnol. 2020, 11, 372–382, doi:10.3762/bjnano.11.28

• . Surprisingly, a remarkable difference was found. CCMV showed a high activation of macrophages, while BMV showed almost no immunogenic response (Figure 3C,D). There is 80% homology in the amino acids sequences of CCMV and BMV [21], however, they differ in their surface charge. The zeta potential at pH 7 was

Using gold nanoparticles to detect single-nucleotide polymorphisms: toward liquid biopsy

• María Sanromán Iglesias and
• Marek Grzelczak

Beilstein J. Nanotechnol. 2020, 11, 263–284, doi:10.3762/bjnano.11.20

• one or a few nucleotides leading to the addition or subtraction of amino acids in the protein. Exon or gene copy-number changes. Large duplications or deletions encompassing entire exons (protein-encoding regions in a gene) and affecting the functional domains of the protein. Structural modifications

• genetic mutations that alter single base in DNA, causing sequence modification in amino acids and malfunction of a corresponding protein. Reprinted with permission from [51], copyright 2014 Elsevier. Gold nanoparticle-based colorimetric assays in the colloidal phase. a) Cross-linking hybridization assay

Internalization mechanisms of cell-penetrating peptides

• Ivana Ruseska and
• Andreas Zimmer

Beilstein J. Nanotechnol. 2020, 11, 101–123, doi:10.3762/bjnano.11.10

• applications in life sciences [8]. In general, CPPs can be defined as diverse peptides with a maximal length of 30 amino acids. They are characterized by a high content of basic amino acids and an overall positive charge. CPPs are known to have a high rate of permeation into cells and are able to cross

• amino acids in the sequence of CPPs as well as their length give rise to the second type of classification. According to these properties, CPPs can be regarded as primary or secondary amphipathic or nonamphipathic peptides. Primary amphipathic peptides contain typically more than 20 amino acids and have

• sequentially hydrophilic and hydrophobic amino acids in their primary structure [5][21]. This group includes MPG, penetratin, CADY, pVec, and other peptides. Secondary amphipathic peptides commonly have less than 20 amino acids in their sequence and are able to take their α-helix or β-sheet conformation after

Fully amino acid-based hydrogel as potential scaffold for cell culturing and drug delivery

• Dávid Juriga,
• Evelin Sipos,
• Orsolya Hegedűs,
• Gábor Varga,
• Miklós Zrínyi,
• Krisztina S. Nagy and
• Angéla Jedlovszky-Hajdú

Beilstein J. Nanotechnol. 2019, 10, 2579–2593, doi:10.3762/bjnano.10.249

• often limits their application. The use of poly(aspartic acid) (PASP) seems an appropriate solution for this problem due to the relatively cheap and simple synthesis of PASP. Using amino acids not only as building blocks in the polymer backbone but also as cross-linkers can improve the biocompatibility

• mainly built from only one or two types of amino acids, are biocompatible nutrients. In addition, poly(amino acid)s have enormous structural diversity and they supposedly lack immunogenicity [24][25]. In summary, the use of poly(amino acid)s has practically only one disadvantage: their synthesis is

• improve the pharmacological and therapeutic properties of various drugs [28]. By applying such microcarriers, the drug release kinetics can be controlled. Among the anionic amino acids, glutamic acid was previously used for the preparation of polymer-based microcarriers [33]. However, there are only

Bombesin receptor-targeted liposomes for enhanced delivery to lung cancer cells

• Mohammad J. Akbar,
• Pâmela C. Lukasewicz Ferreira,
• Melania Giorgetti,
• Leanne Stokes and
• Christopher J. Morris

Beilstein J. Nanotechnol. 2019, 10, 2553–2562, doi:10.3762/bjnano.10.246

• therapeutic outcomes. Experimental Materials Fmoc-protected amino acids, piperazine, HCTU, HOBt, DMF were all from AGTC (Hessle, UK). Rink Amide MBHA resin was from Novabiochem (UK). HPLC solvents and all cell culture media were from Sigma-Aldrich (Poole, UK). Lipids were from Avanti Polar Lipids (USA

• repeated to increase the peptide yield. Successful Fmoc removal and coupling of amino acids was confirmed with the Kaiser test. After successful coupling and Fmoc deprotection of the N-terminal amino acid, the resin was washed with DMF (3 × 5 mL, 1 min), then DCM (3 × 5 mL, 5 min) and the resin dried under

Targeted therapeutic effect against the breast cancer cell line MCF-7 with a CuFe₂O₄/silica/cisplatin nanocomposite formulation

• B. Rabindran Jermy,
• Vijaya Ravinayagam,
• Widyan A. Alamoudi,
• Dana Almohazey,
• Hatim Dafalla,
• Lina Hussain Allehaibi,
• Abdulhadi Baykal,
• Muhammet S. Toprak and
• Thirunavukkarasu Somanathan

Beilstein J. Nanotechnol. 2019, 10, 2217–2228, doi:10.3762/bjnano.10.214

• (100× Gibco, Life Technologies), and 1% MEM non-essential amino acids (NEAA) (100× Gibco, Life Technologies). The cells were kept in a humidified incubator at 37 °C with 5% CO2. For the experimental setup, MCF-7 cells were seeded in a 96-well plate at a density of 20,000 cells/well. On the next day

Review of advanced sensor devices employing nanoarchitectonics concepts

• Katsuhiko Ariga,
• Tatsuyuki Makita,
• Masato Ito,
• Taizo Mori,
• Shun Watanabe and
• Jun Takeya

Beilstein J. Nanotechnol. 2019, 10, 2014–2030, doi:10.3762/bjnano.10.198

• . This sensitivity is sufficient for the detection and monitoring of this persistent pollutant in drinking water. As mentioned previously, the discrimination of chiral substances is a rather tough goal in sensor design. However, the detection of chiral amino acids is an unavoidable matter in technologies

• biomolecules including amino acids [156], peptides [157][158][159], sugars [160][161], nucleic acid bases [162][163], and nucleotides [164][165][166] at well-designed interfacial environments. In order to design and fabricate sensors with better performance, interfacial nanoarchitectonics should be crucial

• used to realize switching recognition selectivity between ʟ- and ᴅ-amino acids [176][177]. Chiral sensing can be tuned by mechanical deformation of the receptor membrane at the interfacial environment. Two-dimensional deformation of cholesterol-substituted triazacyclononane monolayer was used to

Chiral nanostructures self-assembled from nitrocinnamic amide amphiphiles: substituent and solvent effects

• Hejin Jiang,
• Huahua Fan,
• Yuqian Jiang,
• Li Zhang and
• Minghua Liu

Beilstein J. Nanotechnol. 2019, 10, 1608–1617, doi:10.3762/bjnano.10.156

• , amino acids [9][10][11], oligopeptides [12][13], saccharides [14][15][16], steroids [17][18] and diaminocyclohexane derivatives [19][20] have been reported to self-assemble into helical structures, mimicking the natural helical structures found in biological systems. Generally speaking, the common

Materials nanoarchitectonics at two-dimensional liquid interfaces

• Katsuhiko Ariga,
• Michio Matsumoto,
• Taizo Mori and
• Lok Kumar Shrestha

Beilstein J. Nanotechnol. 2019, 10, 1559–1587, doi:10.3762/bjnano.10.153

• ]. Although molecular recognition via hydrogen bonding are quite difficult in a highly polar aqueous media, the molecular recognition of sugars [145][146], peptides [147][148][149], amino acids [150], nucleic acid bases [151][152], and nucleotides [153][154] is accomplishable at the air–water interface even

• conformational changes of molecular receptors at the air–water interface results in a change of the chiral selectivity towards aqueous amino acids [174][175], or of the optimum guest structure from thymine to uracil derivatives [176][177]. Regulation of molecular interaction at liquid interfaces yields a novel

Serum type and concentration both affect the protein-corona composition of PLGA nanoparticles

• Katrin Partikel,
• Robin Korte,
• Dennis Mulac,
• Hans-Ulrich Humpf and
• Klaus Langer

Beilstein J. Nanotechnol. 2019, 10, 1002–1015, doi:10.3762/bjnano.10.101

• -essential amino acids (NEA), 1% (v/v) L-alanyl-L-glutamine (200 mM), and 1% (v/v) penicillin/streptomycin (100 U/mL) (serum-free medium). For the identification of corona proteins by LC–MS/MS analysis a larger particle surface area was required. Thus, 1000 µL of either FBS or human serum were added to an

• cm2 flasks with DMEM supplemented with 10% (v/v) FBS, 1% (v/v) non-essential amino acids (NEA), 1% (v/v) L-alanyl-L-glutamine (200 mM), 1% (v/v) penicillin/streptomycin (100 U/mL) at 37 °C, 100% humidity in a 10% CO2 atmosphere. Cells were subcultivated twice a week at a ratio of approximately 1:5

Outstanding chain-extension effect and high UV resistance of polybutylene succinate containing amino-acid-modified layered double hydroxides

• Adam A. Marek,
• Vincent Verney,
• Christine Taviot-Gueho,
• Grazia Totaro,
• Laura Sisti,
• Annamaria Celli and
• Fabrice Leroux

Beilstein J. Nanotechnol. 2019, 10, 684–695, doi:10.3762/bjnano.10.68

• melt compounding process. The Mg2Al-based PBS nanocomposites, dispersed with inorganic–organic hybrid materials (layered double hydroxides, LDHs), were functionalized with the amino acids L-histidine (HIS) and L-phenylalanine (PHE). The rheological and anti-ultraviolet (anti-UV) properties were

• ]. LDHs are considered to be “green” and low environmental impact fillers [12], biocompatible [13] and food compatible [14]. Indeed the choice of organo-modified LDH using amino acids, and among them the protein-building amino acids, has already been demonstrated [15]. Having in mind that UV stabilization

• should require UV absorption properties for the organic molecule, any proteinogenic amino acids presenting cycle in their backbone will be preferentially considered. Tyrosine and tryptophan have been studied for their UV stabilizing properties; however, histidine (HIS) and (PHE) are rarely reported. One

Mechanical and thermodynamic properties of Aβ₄₂, Aβ₄₀, and α-synuclein fibrils: a coarse-grained method to complement experimental studies

• Adolfo B. Poma,
• Horacio V. Guzman,
• Mai Suan Li and
• Panagiotis E. Theodorakis

Beilstein J. Nanotechnol. 2019, 10, 500–513, doi:10.3762/bjnano.10.51

• of the individual amino-acid chains in these structures. Fibrils consisting of either 40-mer or 42-mer amyloid chains (it contains two additional hydrophobic amino acids) are particularly interesting. For example, Aβ40 typically assembles into two-fold or three-fold symmetries (see Figure 1), while

• achieve this by applying different types of deformation (e.g., tension, shearing and indentation) and analysing the intermolecular contacts between amino acids. Our simulations reveal significant differences in the mechanical behaviour between Aβ40 and Aβ42 and α-syn fibrils. Moreover, we find that the α

• to a van der Waals radius, as proposed by Tsai and co-workers [49]. A sphere with the radius enlarged by a factor of 1.24 is built around the atom. If two amino acids have heavy atoms with overlapping spheres, then we consider a native contact between those two Cα atoms. In Figure 2, we show the CG

Biocompatible organic–inorganic hybrid materials based on nucleobases and titanium developed by molecular layer deposition

• Leva Momtazi,
• Henrik H. Sønsteby and
• Ola Nilsen

Beilstein J. Nanotechnol. 2019, 10, 399–411, doi:10.3762/bjnano.10.39

• previous study on organic–inorganic MLD materials, in which we used amino acids as organic linkers to form titaminates [22]. We here build on that knowledge and expand the range of bioactive MLD materials to now include nucleobases as organic linkers. The films have been prepared by combining titanium

• tetra-isopropoxide (TTIP) with thymine, uracil, and adenine (Figure 1). We have recently reported a significant increase in the proliferation rate of rat conjunctival goblet cells cultured on substrates coated with these hybrid materials based on amino acids, and also the currently presented nucleobases

• , respectively. The increase in refractive index with temperature is similar to what we observed for the Ti-amino acids films in our previous study while the density of these materials was less affected by temperature as compared to the density of the Ti-nucleobase films [22]. After one day of exposure in air

Mechanism of silica–lysozyme composite formation unravelled by in situ fast SAXS

• Tomasz M. Stawski,
• Daniela B. van den Heuvel,
• Rogier Besselink,
• Dominique J. Tobler and
• Liane G. Benning

Beilstein J. Nanotechnol. 2019, 10, 182–197, doi:10.3762/bjnano.10.17

• of the opposite active sites in the side-on orientation (i.e., both active sites show similar binding properties). In such a case one should indeed expect the DLPCA mode of aggregation, with the binding of the protein to the silica NP surfaces taking place through specific amino acids at the opposite

A novel polyhedral oligomeric silsesquioxane-modified layered double hydroxide: preparation, characterization and properties

• Xianwei Zhang,
• Zhongzhu Ma,
• Hong Fan,
• Carla Bittencourt,
• Jintao Wan and
• Philippe Dubois

Beilstein J. Nanotechnol. 2018, 9, 3053–3068, doi:10.3762/bjnano.9.284

• ][19], amino acids [20], anionic dyes [11], and compounds of biological origin, such as β-cyclodextrin and eugenol derivatives [9][10][13][21]. However, most of these current modifiers do not have satisfactory thermal stability and are flammable, reducing the thermal and fire stability of the LDHs

Colloidal chemistry with patchy silica nanoparticles

• Pierre-Etienne Rouet,
• Cyril Chomette,
• Laurent Adumeau,
• Etienne Duguet and
• Serge Ravaine

Beilstein J. Nanotechnol. 2018, 9, 2989–2998, doi:10.3762/bjnano.9.278

• colloidal molecules The binding of the aminated dimpled particles with the satellites is based on amide bonding, i.e., peptidic coupling, extensively studied in biochemistry for the modification of amino acids [25]. The carboxylic groups are not reactive enough toward amino groups, and a simple and well