Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• tryptophan, the equilibrium between the monomer and the oligomer formation is shifted towards the latter [75][76]. Examples of PPIs within higher-order protein complexes PPIs are responsible for the assembly of large protein complexes, such as capsid proteins in viruses and protein containers. This section

• will give a brief overview on how such interactions can give rise to these complex molecules. Capsid viruses The infectivity in viruses is dependent on the correct assembly of viral capsids and surface proteins. A virus is made up of a genome enclosed by a number of copies of proteins to form a shell

• known as a capsid [78]. Some viruses also have lipid envelopes containing glycoproteins, which interact with the host cell membrane to facilitate the viral entry into the cell [79]. The simplest explanation for viral capsid assembly is protein assembly units colliding (following Brownian motion) in a

Secondary metabolites of Bacillus subtilis impact the assembly of soil-derived semisynthetic bacterial communities

• Heiko T. Kiesewalter,
• Carlos N. Lozano-Andrade,
• Mikael L. Strube and
• Ákos T. Kovács

Beilstein J. Org. Chem. 2020, 16, 2983–2998, doi:10.3762/bjoc.16.248

• proliferating under the given conditions and independently from other bacteria. During the following 48 h cocultivation, depletion of the primary nutrient sources and metabolic cross-feeding further shaped the community assembly. In 2018, Goldford et al. revealed that the main sources of metabolic cross-feeding

• are secreted metabolic byproducts from the community members [57]. They further highlighted that bacterial communities stabilised after approximately eight to nine 48 h cocultivations. In our study, bacterial communities were only cocultivated once for 48 h, suggesting that the assembly of the

• prolonged incubation. The B. subtilis strains were added at a community assembly phase when Bacillus was the dominating genus, so that the general genera distribution was not expected to be influenced extensively. Nevertheless, after 48 h cocultivation, the final relative abundance of the Bacillus genus was

Construction of pillar[4]arene[1]quinone–1,10-dibromodecane pseudorotaxanes in solution and in the solid state

• Xinru Sheng,
• Errui Li and
• Feihe Huang

Beilstein J. Org. Chem. 2020, 16, 2954–2959, doi:10.3762/bjoc.16.245

• constructing functional materials from the bottom up as well as an important way to create new substances with functions [1][2][3][4][5]. Through ingenious designs and the applications of molecular recognition and self-assembly strategies, many exquisite supramolecular architectures have been fabricated

Using multiple self-sorting for switching functions in discrete multicomponent systems

• Amit Ghosh and
• Michael Schmittel

Beilstein J. Org. Chem. 2020, 16, 2831–2853, doi:10.3762/bjoc.16.233

• self-sorting protocols. The present mini review will provide an overview over the latest advancements in this field with a focus on reversibly switchable functions in discrete supramolecular systems. Keywords: copper; fluorescence; self-assembly; self-sorting; zinc porphyrin; Introduction Since self

• self-assembly of the triamines 10 and 11 in the presence of the aldehyde 12 and cobalt(II) ions [52]. When all components were mixed in a single reaction vessel, the 1H NMR spectrum indicated the formation of homoleptic as well as heteroleptic species. In the following, they explored the ability of the

• of various similar molecules. Similarly, Shi controlled a conversion between helicates and a tetrahedral cage by varying the radius of the metal ion (Hg2+ vs Fe2+) [55]. They reported on the self-assembly of the monomer 20, encompassing the quadruple DDAA hydrogen-bonding arrays and 2,2’-bipyridine

Easy access to a carbohydrate-based template for stimuli-responsive surfactants

• Thomas Holmstrøm,
• Daniel Raydan and
• Christian Marcus Pedersen

Beilstein J. Org. Chem. 2020, 16, 2788–2794, doi:10.3762/bjoc.16.229

• distance of the two lipophilic tails resulting in a self-assembly of the molecules into larger aggregates that could be characterized with DLS and TEM [11]. In a previous study by Yuasa et al., it was shown that the distance between the two groups on the anomeric and the 3-position indeed decreased upon a

Encrypting messages with artificial bacterial receptors

• Pragati Kishore Prasad,
• Naama Lahav-Mankovski,
• Leila Motiei and
• David Margulies

Beilstein J. Org. Chem. 2020, 16, 2749–2756, doi:10.3762/bjoc.16.225

• simpler way to modify the bacterial membrane is by adding to X-ODN-1 a complementary strand (Y-ODN-2) that is modified with the desired functionality (Y) (Figure 1A). In this way, the structure of the artificial receptors can be ‘programmed’ by a simple self-assembly process, which provides the means to

Selective recognition of ATP by multivalent nano-assemblies of bisimidazolium amphiphiles through “turn-on” fluorescence response

• Rakesh Biswas,
• Surya Ghosh,
• Shubhra Kanti Bhaumik and
• Supratim Banerjee

Beilstein J. Org. Chem. 2020, 16, 2728–2738, doi:10.3762/bjoc.16.223

• to an n-alkyl chain at the other, underwent self-assembly in aqueous media depending on the length of the alkyl segment. The amphiphilic derivatives having n-decyl or longer chains, formed nano-assemblies with cyanic–green emission resulting from the stacked pyrene chromophores in the aggregates. The

• buffer and also in buffer containing 150 mM NaCl at physiological pH value. Furthermore, the multivalent aggregates demonstrated a significant selectivity in ATP detection over ADP, AMP and pyrophosphate. Keywords: amphiphile; ATP; excimer; multivalency; self-assembly; Introduction Supramolecular anion

• ]. In this methodology, multivalent arrays are built from comparatively smaller binding sites through self-assembly. The smaller molecular units are easier to synthesize and moreover, the morphology and the surface functionalities of the resultant multivalent structures can be tuned in a modular fashion

Enzyme-instructed morphological transition of the supramolecular assemblies of branched peptides

• Dongsik Yang,
• Hongjian He and
• Bing Xu

Beilstein J. Org. Chem. 2020, 16, 2709–2718, doi:10.3762/bjoc.16.221

• cellular environment. Keywords: acetylation; branched peptides; enzyme; nanostructures; N-terminal; responsive; self-assembly; Introduction Peptides, being able to self-assemble to exhibit emergent properties and functions [1][2][3][4][5], have received considerable attentions recently. For example

• utilizes nonlinear peptides. For example, nonribosomal peptides exist in other geometries, such as branched (e.g., bleomycin) or cyclic peptides (e.g., vancomycin) [31]. While the understanding of the synthesis of branched peptides is well-developed, the self-assembly and enzymatic conversion of branched

• peptides has received limited attention [2][32][33][34][35][36][37]. For example, Stupp et al. reported that a cell adhesion epitope, RGDS, acts as a branch to peptide amphiphiles for making hydrogels via self-assembly [34][36]. Ulijn et al. connected Fmoc-DAARRGG to a lysine side chain for incorporation

A heterobimetallic tetrahedron from a linear platinum(II)-bis(acetylide) metalloligand

• Matthias Hardy,
• Marianne Engeser and
• Arne Lützen

Beilstein J. Org. Chem. 2020, 16, 2701–2708, doi:10.3762/bjoc.16.220

• (acetylide)platinum(II) complex [Pt(L1)2(PBu3)2] as a linear metalloligand. The reaction of this metalloligand with iron(II) cations and pyridine-2-carbaldehyde according to the subcomponent self-assembly approach yielded decanuclear heterobimetallic tetrahedron [Fe4Pt6(L2)12](OTf)8. Thus, combination of

• these two design concepts – the subcomponent self-assembly strategy and the complex-as-a-ligand approach – ensured a fast and easy synthesis of large heterobimetallic coordination cages of tetrahedral shape with a diameter of more than 3 nm as a mixture of all three possible T-, S4- and C3-symmetric

• complexes; pyridylimine ligands; self-assembly; supramolecular chemistry; Introduction The understanding of the general design principles for the self-assembly of metallosupramolecular aggregates [1][2][3][4][5] allowed to access more and more complex and large assemblies over the past decades like

Optical detection of di- and triphosphate anions with mixed monolayer-protected gold nanoparticles containing zinc(II)–dipicolylamine complexes

• Lena Reinke,
• Julia Bartl,
• Marcus Koch and
• Stefan Kubik

Beilstein J. Org. Chem. 2020, 16, 2687–2700, doi:10.3762/bjoc.16.219

• thus caused the disassembly rather than the assembly of the AuNPs) [34]. While the limit of detection was sometimes very good (in one case less than 0.2 μmol/L [31]), these systems mostly involved the combination of several components and the analyte was in some cases only detected indirectly. In

Water-soluble host–guest complexes between fullerenes and a sugar-functionalized tribenzotriquinacene assembling to microspheres

• Si-Yuan Liu,
• Xin-Rui Wang,
• Man-Ping Li,
• Wen-Rong Xu and
• Dietmar Kuck

Beilstein J. Org. Chem. 2020, 16, 2551–2561, doi:10.3762/bjoc.16.207

• of 0.3–3.5 μm were observed for the complex TBTQ-(OG)6 C60. Obviously, these aggregates form by further assembly of the supra-amphiphilic host–guest systems, as suggested in Figure 6c, due to the hydrophobic interactions governing the association behavior of TBTQ-(OG)6 C60 in water. Conclusion In

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• they have been used to serve as scaffolds for the assembly of protein arrays and crystallization aids [23][24][25][26][27][28]. In addition, a terbiumIII complex termed crystallophore has been developed as a crystallographic nucleation and phasing tool for protein crystallography that can also easily

• monomeric in solution with the small calix[4]arene, while calix[6]arene induces protein dimerization [23], and calix[8]arene even tetramerization [24] in solution as evidenced by SEC-MALS. In the NMR spectra, the assembly of proteins is evident by increased line broadening of most residues due to the

Host–guest interaction of cucurbit[8]uril with oroxin A and its effect on the properties of oroxin A

• Zhishu Zeng,
• Jun Xie,
• Guangyan Luo,
• Zhu Tao and
• Qianjun Zhang

Beilstein J. Org. Chem. 2020, 16, 2332–2337, doi:10.3762/bjoc.16.194

• that the molecular size of the flavonoids and the length of the sugar chains have a greater impact on the assembly mode of supramolecular systems. Results and Discussion Host–guest interactions The host–guest interaction can be effectively observed using 1H NMR spectroscopy, and the mode of action of

The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY

• Patrizia Andreozzi,
• Lorenza Tamberi,
• Elisamaria Tasca,
• Gina Elena Giacomazzo,
• Marta Martinez,
• Mirko Severi,
• Marco Marradi,
• Stefano Cicchi,
• Sergio Moya,
• Giacomo Biagiotti and
• Barbara Richichi

Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188

• their derivatives have been widely used in biomedical applications, especially as drug and gene carriers, both in hydrogels and in nanoparticulate formulations [29][30][31][32]. In this regard, the incorporation of hydrophobic moieties in the branched structure of dextrans induces self-assembly into

• short reaction time, reactant economy, higher degree of functionalization, and solvent-free conditions, compared to solution-based routes are discussed. The dextran mechanochemically conjugated to PBA-BODIPY (Dex-1b, Figure 1) formed nanoparticles through self-assembly retaining the fluorescent

Synthetic approaches to bowl-shaped π-conjugated sumanene and its congeners

• Shakeel Alvi and
• Rashid Ali

Beilstein J. Org. Chem. 2020, 16, 2212–2259, doi:10.3762/bjoc.16.186

• -assembly, and optical properties of bowl-shaped π-conjugated systems [5][6][7][8][9]. The synthesis of π-bowls is an extremely challenging job due to the presence of unusual strain in these types of molecules, therefore, the first synthetic breakthrough in this arena came into the picture in the late

• the self-assembly. This was confirmed by single crystal structure and it was noticed that all 15 carbon atoms of the three Cp-types of the ring were interacted with the metal atoms and the six K atoms were sandwiched between the convex faces of two sumanenyl trianions. On the other hand, two years

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• drug delivery, tissue engineering and regeneration, and as stimuli-responsive materials. Herein, we report the pH- and concentration-dependent self-assembly and conformational transformation of the newly synthesized octapeptide PEP-1. At pH 7.4, PEP-1 forms β-sheet-rich secondary structures into

• and resulting morphologies due to electrostatic repulsion between charged amino acids. PEP-1 can also form helical or random-coil secondary structures at a relatively low concentration. The obtained pH-sensitive self-assembly behavior of the target octapeptide is expected to contribute to the

• development of novel drug nanocarrier assemblies. Keywords: aqueous self-assembly; pH-responsive systems; secondary structure; self-assembled nanostructures; solid-phase peptide synthesis; Introduction The self-assembly of small molecules is a ubiquitous phenomenon in nature [1] and also has key

Controlling the stereochemistry in 2-oxo-aldehyde-derived Ugi adducts through the cinchona alkaloid-promoted electrophilic fluorination

• Yuqing Wang,
• Gaigai Wang,
• Anatoly A. Peshkov,
• Ruwei Yao,
• Muhammad Hasan,
• Manzoor Zaman,
• Chao Liu,
• Stepan Kashtanov,
• Olga P. Pereshivko and
• Vsevolod A. Peshkov

Beilstein J. Org. Chem. 2020, 16, 1963–1973, doi:10.3762/bjoc.16.163

• dichloromethane results in the assembly of an α-acyloxyamide adduct 4. Just a few protocols for the asymmetric P-3CR [37][38][39][40] and its modifications [41][42][43][44][45][46][47] have been reported over the course of the last two decades (Table 1). In the majority of those protocols [37][38][39], the

• -aldehyde 7. For example, we have explored the potential of the peptidyl reactive site in a number of enolization-driven post-Ugi cyclizations leading to the assembly of pyrrol-2-ones 9 and 10 [59][60]. We have also taken advantage of a 1,3-dicarbonyl moiety present in 8 by engaging them in an enolization

Facile synthesis of 7-alkyl-1,2,3,4-tetrahydro-1,8-naphthyridines as arginine mimetics using a Horner–Wadsworth–Emmons-based approach

• Rhys A. Lippa,
• John A. Murphy and
• Tim N. Barrett

Beilstein J. Org. Chem. 2020, 16, 1617–1626, doi:10.3762/bjoc.16.134

• deuteration. Conclusion In conclusion, a novel method for the assembly of 7-alkyl-1,2,3,4-tetrahydro-1,8-naphthyridine-based arginine mimetics was developed. The synthesis of phosphonate 7 was optimised, with a sequential diphosphorylation process using commercially available starting materials affording the

A dynamic combinatorial library for biomimetic recognition of dipeptides in water

• Florian Klepel and
• Bart Jan Ravoo

Beilstein J. Org. Chem. 2020, 16, 1588–1595, doi:10.3762/bjoc.16.131

• interaction of the dipeptides with themselves. For example, FF is a popular self-assembly motif, which also explains its poor solubility (≈5 mM) [23]. Hence the thermodynamic data depicts not only the association of a(CFC)2/p(CFC)2 towards FF, but also the dissociation of FF assemblies. The aromatic side

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• -bonding interactions, the narrow π–π stacking provides a sufficient π orbital overlap to produce semiconductor-type electronic band structures and an efficient interplanar charge transport similar to g-C3N4 [192]. Duan and co-workers reported the synthesis of a zinc PDI assembly as a heterogeneous

Disposable cartridge concept for the on-demand synthesis of turbo Grignards, Knochel–Hauser amides, and magnesium alkoxides

• Mateo Berton,
• Kevin Sheehan,
• Andrea Adamo and
• D. Tyler McQuade

Beilstein J. Org. Chem. 2020, 16, 1343–1356, doi:10.3762/bjoc.16.115

• –Hauser bases synthesis using a stratified packed-bed column of activated magnesium and lithium chloride.a Comparison between batch [47][67] and flow conditions for the synthesis of (TMPMgCl⋅LiCl). Supporting Information All details for the flow procedures and reactors assembly (full part list, flow

Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole

• Carlos H. Escalante,
• Eder I. Martínez-Mora,
• Carlos Espinoza-Hicks,
• Alejandro A. Camacho-Dávila,
• Fernando R. Ramos-Morales,
• Francisco Delgado and
• Joaquín Tamariz

Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113

• intermolecular interactions (NCIs) between aromatic rings (π···π) [58][59] and alkyl and aromatic ring (Csp3–H)···π stackings [59][60][61][62] are widely recognized, from both the experimental and theoretical viewpoint, as a major factor governing the conformational equilibrium, supramolecular assembly and

Activated carbon as catalyst support: precursors, preparation, modification and characterization

• Melanie Iwanow,
• Tobias Gärtner,
• Volker Sieber and
• Burkhard König

Beilstein J. Org. Chem. 2020, 16, 1188–1202, doi:10.3762/bjoc.16.104

• aerosol-assisted self-assembly using amphiphilic triblock copolymers as template and low-molecular weight soluble phenol resin as carbon source. The amphiphilic surfactant influences the pore size and mesostructure of the resulting spherical carbons. Finally, the template is removed by calcination [97

A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA

• Ekaterina A. Bryushkova,
• Erik R. Gandalipov and
• Julia V. Nuzhina

Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100

• cited by Silverman 2016 [19]; the green star indicates a malachite green dye molecule. C) Malachite green dye chemical structure. D) Detailed malachite green split aptamer structure cited by Kolpaschikov 2005 [20]. E) Confirmation of SDFS assembly by using agarose gel electrophoresis; lane 1: DNA ladder

Synthesis of new asparagine-based glycopeptides for future scanning tunneling microscopy investigations

• Laura Sršan and
• Thomas Ziegler

Beilstein J. Org. Chem. 2020, 16, 888–894, doi:10.3762/bjoc.16.80

• self-assembly on metal surfaces [16][17]. For such novel MS applications, a new technology, i.e., ES-IBD, has been developed. ES-IBD furthermore allows for the integrity of the material [18]. The application of these new techniques to synthetic glycopeptides is expected to provide new insight into the

• investigation of the self assembly of such glycopeptides on metal surfaces will be performed via pMS and STM in further studies. Description of the starting materials 1a–f and 2a–f. Peptide coupling reactions, including the previous Fmoc cleavage. Cleavage of the fully protected peptides 6 and 7. Yields of the