Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• option to modulate, inhibit, or stabilize protein–protein interactions (PPI) is the use of specific supramolecular ligands [7][8]. One well-known example of efficient protein binders is the so-called guanidiniocarbonyl-pyrrole (GCP) developed 20 years ago by Schmuck et al. [9]. These compounds are known

• -anions [11]. The guanidiniocarbonyl-pyrrole (GCP) is able to bind oxo-anions even in aqueous solvents with competing ions and salts. Schmuck et al. also discovered that an additional positive charge increases the binding affinity to oxo-anions [10]. These unique properties make the GCP oxo-anion binder

• an ideal candidate to be used for protein recognition. In a previous study, GCP containing polycationic ligands for 14-3-3 proteins had a significant effect on PPIs [12][13]. Furthermore, a simple GCP derivative, GCP-Lys-OMe, was identified as the first binder for the specific binding area of the 14

A tribute to Carsten Schmuck

• Jochen Niemeyer,
• Ivo Piantanida and
• Thomas Schrader

Beilstein J. Org. Chem. 2021, 17, 2795–2798, doi:10.3762/bjoc.17.190

• , we agreed to try Carsten’s guanidiniocarbonylpyrrole (GCP) cation system in our group for DNA/RNA recognition. In that way, we started our collaboration and exchange of students which was, thanks to Carsten’s great personality, very pleasant and friendly. Moreover, due to Carsten’s profound knowledge

• into account particular features of “Carsten’s GCP” unit, or related analogues, he would propose several feasible structural modifications, which could provide novel properties of scientific interest. Finally, upon mutually agreeing on the next generation of new compounds, he would always take the

A sustainable strategy for the straightforward preparation of 2H-azirines and highly functionalized NH-aziridines from vinyl azides using a single solvent flow-batch approach

• Michael Andresini,
• Leonardo Degannaro and
• Renzo Luisi

Beilstein J. Org. Chem. 2021, 17, 203–209, doi:10.3762/bjoc.17.20

• and potentially automatable method for the synthesis of interesting strained compounds. Keywords: aziridines; 2H-azirines; flow chemistry; green chemistry; organolithium compounds; Introduction Since their conception in the early 1990s, Green Chemistry Principles (GCP) have been applied with

• to the large surface–volume ratio of microreactors, and may prevent the formation of undesirable byproducts that are not avoidable under the traditional batch conditions. As a consequence, efforts have been devoted to the development of synthetic processes combining GCP and enabling technologies [11

Supramolecular polymers with reversed viscosity/temperature profile for application in motor oils

• Jan-Erik Ostwaldt,
• Christoph Hirschhäuser,
• Stefan K. Maier,
• Carsten Schmuck and
• Jochen Niemeyer

Beilstein J. Org. Chem. 2021, 17, 105–114, doi:10.3762/bjoc.17.11

• acid (GCP) or the aminopyridine carbonyl pyrrole carboxylic acid (ACP). At low temperatures, small cyclic structures are formed. However, at elevated temperatures, a ring–chain transformation leads to the formation of a supramolecular polymer. We demonstrate that this effect is dependent on the

• VII system requires a BU with strong dimerization tendency and a LU with precoordinating properties. For our purpose, we initially employed the guanidiniocarbonyl pyrrole (GCP) motif as a binding unit [19]. The GCP unit is a self-complementary zwitterion, which forms dimers with high association

• constants, based on a sixfold hydrogen-bonding interaction, strengthened by coulombic interactions (see Figure 2a) [20][21]. The GCP motif has successfully been applied for the formation of supramolecular polymers in earlier works [22][23][24][25]. The ionic nature of the GCP motif allows self-pairing even

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• peptidic arms equipped with lysine and an artificial strong anion binding site, the guanidinocarbonylpyrrole (GCP) moiety (Figure 2A). These arms also contain tryptophan for dissimilar aromatic interactions with different nucleobases. The fluorescence intensity of probe 1 increases by more than 4-fold at

• binding GCP moiety. In between these two arms, a fluorophore (aminonaphthalimide for 4 and diethylaminocoumarin for 5) is linked to a third arm. Compounds 4 and 5 are weakly fluorescent and show significant “switch-on” fluorescence response upon interaction with dsDNA (Figure 5B). Probe 4 shows preference

• involved in a variety of human diseases like cancer, Alzheimer’s, and Parkinson diseases etc. [46]. Therefore, the Schmuck group in collaboration with the Ottmann group sought to develop fluorescent probes (7 and 8) for monitoring of 14-3-3 proteins (Figure 7) [47]. These probes contain two symmetric GCP

UV resonance Raman spectroscopy of the supramolecular ligand guanidiniocarbonyl indole (GCI) with 244 nm laser excitation

• Tim Holtum,
• Vikas Kumar,
• Daniel Sebena,
• Jens Voskuhl and
• Sebastian Schlücker

Beilstein J. Org. Chem. 2020, 16, 2911–2919, doi:10.3762/bjoc.16.240

• UVRR approach from peptides to proteins as binding partners for GCPs is the UV-excited autofluorescence from aromatic amino acids observed for laser excitation wavelengths >260 nm. These excitation wavelengths are in the electronic resonance with the GCP for achieving both a signal enhancement and the

• autofluorescence of the peptide or protein. Here, we demonstrate the use of UVRR spectroscopy with 244 nm laser excitation for the characterization of GCP as well as guanidiniocarbonyl indole (GCI), a next generation supramolecular ligand for the recognition of carboxylates. For demonstrating the feasibility of

• the results from density functional theory (DFT) calculations. Keywords: GCI; GCP; guanidiniocarbonyl indole; guanidiniocarbonyl pyrrole; UVRR; Raman spectroscopy; resonance Raman; Introduction Supramolecular ligands are capable to selectively bind to peptides and proteins via reversible non

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

• ], guanidiniocarbonylpyrrole (GCP) ligands [41][42][43][44][45][46], cucurbiturils [47][48][49][50][51], porphyrins [52][53][54][55][56][57][58][59][60], metal complexes [61][62][63], foldamers [64][65][66][67], nanoparticles [34][68], imprinted polymers [69][70][71][72], and dendrimers [73][74]. In this review, we focus

• guanidinocarbonylpyrrole (GCP)-based ligands [41]. GCP mimics the natural amino acid arginine binding to the carboxylate side chains of aspartate (Asp) and glutamate (Glu). The GCP unit provides an extended hydrogen bonding/salt bridge interface, which leads to better binding compared to its natural counterpart. The

• combination of two or more GCP moieties with variable linkers enables the construction of multivalent ligands geared towards a specific spot on protein surface, which by design can lead to either stabilization [42][43][44][45] or inhibition [46] of a given protein–protein interaction. The inhibition of the

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• naphthalene diimde analogue (NDI) equipped at the imide positions with two guanidinio-carbonyl-pyrrole (GCP) pendant arms interacted significantly stronger with ds-DNA at pH 5 than at pH 7, due to reversible protonation of the GCP arms. This was consequence of a pH-switchable threading intercalation into ds

• -DNAs only at pH 5, while at neutral conditions (pH 7) NDI-GCP2 switched to the DNA minor groove binding. Intriguingly, NDI-GCP2 was at both pH values studied bound to the ds-RNA major groove, still showing a higher affinity and thermal denaturation effect at pH 5 due to GCP protonation. At excess over

• spectroscopy methods (FDCD, CPL), the sensitivity of response is approaching the classical fluorimetric probes [14]. Our systematic work on aryl-guanidiniocarbonyl-pyrrole (GCP) derivatives characterised the GCP moiety as very useful building block in the design of new small molecules targeting DNA/RNA. The

Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA

• Annike Weißenstein,
• Myroslav O. Vysotsky,
• Ivo Piantanida and
• Frank Würthner

Beilstein J. Org. Chem. 2020, 16, 2032–2045, doi:10.3762/bjoc.16.170

• -(trimethylammonium)ethylamine instead of an amino acid (Figure 1) was prepared. In our study of the interactions with DNA/RNA weakly acidic conditions (pH 5) were chosen to complement available pH-dependent AA-fluorophores used in our previous research (PHEN-AAs [12][26] and GCP-derivatives [15][27]), which allowed

• of the water-soluble NDIs The spectrophotometric properties of the NDIs 3a,b, and 5 were investigated in cacodylate buffer at pH 5.0 for easier comparison with complementary pH-dependent AA–fluorophores used in our previous research (PHEN–AAs [26] and GCP derivatives [27]). Additionally, the

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• )pyrrole (GCP) cation 1 as a synthetic analogue of the guanidinium cations, somehow a “super-guanidinium” conceived to drive “arginine magic” [20][21] to the extreme (Figure 1) [23]. The power of the Schmuck cation to bind carboxylate and phosphate anions in competitive water has several origins [22

• binding is further enhanced by the addition of hydrogen-bonding interactions between the amide NH moiety in position 5 of the pyrrole ring or the pyrrole NH group and the oxoanion (Figure 1, blue part). Thirdly, the rigid and planar conformation of the GCP moiety is beneficial to bind planar anions such

• as carboxylate (Figure 1, red part). Finally, the selectivity and specificity for different substrates can be achieved through the additional secondary interactions between the GCP side chain and the anionic substrates (Figure 1, green part). The binding of the Schmuck cation with carboxylates in

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• “cyanostar” macrocycle [15][16]. Although not a macrocycle, a successful binding motif that is noteworthy for its ability to bind carboxylates in polar environments, is the guanidiniocarbonylpyrrole (GCP) moiety designed by Carsten Schmuck and Michael Schwegmann [17]. The transition from complexation studies