[2 + 1] Cycloaddition reactions of fullerene C₆₀ based on diazo compounds

• Yuliya N. Biglova

Beilstein J. Org. Chem. 2021, 17, 630–670, doi:10.3762/bjoc.17.55

• the main characteristics of C60 stimulated a great interest in the application of fullerenes in medical chemistry. Of the fullerene-based biologically significant molecules, amino acid derivatives are of particular interest. In fact, Prato and co-workers synthesized and characterized the first peptide

• amphiphilic C60 derivatives. Treatment of 14 with oxalyl chloride gives reactive acid chloride 15. Acylation of the presynthesized (ʟ-Ala-Aib)2-ʟ-Ala-OMe peptide with compound 15 gives the expected fullerene–peptide conjugate 16 (Scheme 8). A somewhat modified version for the synthesis of peptidofullerenes is

• given in Scheme 9 [87]. On this pathway for the synthesis of conjugates 19 and 20, acid 18 is cross-linked with a peptide component using a milder carbodiimide method via the starting methanofullerene 17. Similar to Scheme 8, fullerene adducts 21 and 22 with glycine and phenylalanine, respectively, were

Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases

• Naohiro Horie,
• Takao Yamaguchi,
• Shinji Kumagai and
• Satoshi Obika

Beilstein J. Org. Chem. 2021, 17, 622–629, doi:10.3762/bjoc.17.54

• synthesis of 2'-amino-LNA (Figure 1) functionalized with a peptide or sugar at the N2'-position, with the aim of modulating the physicochemical properties and specific organ distributions of the therapeutic oligonucleotides [13][14]. A more favorable example is the covalent attachment of a guanidine moiety

Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

• Masayori Hagimori,
• Estefanía E. Mendoza-Ortega and
• Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

• Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan 10.3762/bjoc.17.45 Abstract Ligand-targeted microbubbles are focusing interest for molecular imaging and delivery of chemotherapeutics. Lipid–peptide conjugates (lipopeptides) that feature alternating

• . By contrast, the hydrocarbon lipopeptide led to microbubbles with a larger mean diameter and a significantly lower stability. Keywords: adsorption at fluid interfaces; drug delivery; microbubble targeting; molecular imaging; monolayer; perfluoroalkylated lipopeptide; solid-phase peptide synthesis

• particular cell surface receptor [7][9][10][11][12][13][14]. To this aim, ligand–lipid conjugates have been developed in research and preclinical development for liposome targeting for decades. In particular, peptide ligands offer significant advantages, including efficient synthesis routes, versatility, and

Synthetic strategies of phosphonodepsipeptides

• Jiaxi Xu

Beilstein J. Org. Chem. 2021, 17, 461–484, doi:10.3762/bjoc.17.41

• phosphonodepsipeptides with C-1-hydroxyalkylphosphonic acids. Keywords: alkylation; mimetic; multicomponent condensation; peptide; phosphonopeptide; phosphonodepsipeptide; phosphonylation; Introduction Both, phosphonopeptides and phosphonodepsipeptides are phosphorus analogues of peptides [1][2][3][4][5]. The

• acids and hydroxy esters through phosphonochloridates as in situ-generated intermediates. To prepare an antigen to induce monoclonal catalytic antibodies capable of catalyzing peptide-bond formation reactions, the phosphonodepsidipeptide 39 was synthesized via the coupling of the hydroxy analog of

• , another library of phosphonodepsipeptides 78 was prepared (Scheme 12) [27]. Synthesis of γ-phosphonodepsipeptides γ-Phosphonodepsipeptides 79 have been prepared from N-Cbz-ʟ-glutamic acid (80) and diethyl 2-hydroxyglutarate (84). To prepare phosphorus analogues of γ-glutamyl peptide, the starting N-Cbz-ʟ

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

• , while the remaining C–H bond in Flp acquires an enhanced positive charge due to the electron-withdrawing effect of fluorine. Based on these considerations, a fluoroproline–aromatic-system interaction has been previously utilized in the engineering of a few peptide therapeutics [44][45]. 2.3

• proline is the comparatively similar intrinsic stability of the amide rotamers in the peptidyl-prolyl fragments. Usually, a peptide bond exhibits a high preference towards the trans-amide, represented by a dihedral angle ω of 180°. In peptidyl-prolyl, however, trans- and cis-conformations (ω = 180° and 0

• (Figure 10B). If the mRNA codon matches the anticodon of the tRNAPro, GTP undergoes hydrolysis, allowing the elongation factor Tu to leave the complex. This event is followed by the peptidyl transfer reaction, which forms a new peptide bond. Subsequently, the ribosome binds the elongation factor G

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• tyrosine [16] (pFtBTyr, 9) and proline [17] (4R and 4S-pFtBHyp, 10 and 11, Figure 1) have also been utilised as 19F NMR probes, both showing promise as valuable tools for biomolecular studies. Particularly impressive is that by incorporating pFtBTyr (9) into a model peptide, Tressler and Zondlo were able

• to detect the presence of a sharp singlet in the 19F NMR spectrum even at nanomolar peptide concentrations. It is worth noting here that, as recently reviewed in detail by Koksch [18][19], while some perfluorinated amino acids such as hexafluoroleucine (12, Figure 1) and pentafluorophenylalanine (13

• estrogen receptor (ER) co-activator peptides and enabled the sensitive detection of their protein–peptide interaction inhibition by the ER antagonist tamoxifen [20]. Significantly, different secondary structure conformational preferences were also found among the diastereomers of perfluoro-tert

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• Research Center of Electron Microscopy, Freie Universität Berlin, Fabeckstr. 34a, 14195 Berlin 10.3762/bjoc.17.10 Abstract The synthesis of a sulfate-modified dendritic peptide amphiphile and its self-assembly into one-dimensional rod-like architectures in aqueous medium is reported. The influence of the

• self-assembly turns out to be crucial in obtaining supramolecular polymers suitable for interactions with biological targets [16]. Peptide amphiphiles provide access to supramolecular structures in this competitive environment by taking advantage of nature’s versatile toolbox of noncovalent

• recently reported the successful application of functional supramolecular polymers in a biological context [30]. By decoration of the discotic peptide amphiphile monomers with dendritic mannose moieties, a specific cell targeting of macrophages and internalization in those antigen presenting cells has been

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

• incorporated deuterium can then be localised through protease-generated peptide fragments or fragmentation within the mass spectrometer. The rate of hydrogen-to-deuterium exchange provides insight into the solvent accessibility. HDXMS provides information on the conformation of the protein, PPIs, and even

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• complex, reflecting the high structural diversity of peptide and glycan portions. The use of glycopeptide-centered glycoproteomics by mass spectrometry is rapidly evolving in many research areas, leading to a demand in reliable data analysis tools. In recent years, several bioinformatic tools were

• compared to Skyline, and GlycopeptideGraphMS. All quantification packages resulted in comparable glycosylation profiles but featured differences in terms of robustness and data quality control. Partial cysteine oxidation was identified as an unexpectedly abundant peptide modification and impaired the

• separation of glycopeptides in RPLC is mainly driven by the peptide portions. Thus, information on different proteins and glycosylation sites appears in the form of glycopeptide clusters. Next to the peptide portion, glycosylation features, such as sialic acids, can strongly influence the retention time [8

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

• Bacillus spp. produce various SMs [33][34]. The most prominent and bioactive SMs are nonribosomal peptides (NRPs), of which isoforms belong to the families of surfactins, fengycins, or iturins [35][36] (Figure 1). They are biosynthesised by large enzyme complexes, nonribosomal peptide synthetases (NRPSs

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

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

• Debabrata Maity Department of Chemistry, New York University, New York, NY 10003, USA 10.3762/bjoc.16.247 Abstract To understand the molecular interactions, present in living organisms and their environments, chemists are trying to create novel chemical tools. In this regard, peptide-based

• fluorescence techniques have attracted immense interest. Synthetic peptide-based fluorescent probes are advantageous over protein-based sensors, since they are synthetically accessible, more stable, and can be easily modified in a site-specific manner for selective biological applications. Peptide receptors

• labeled with environmentally sensitive/FRET fluorophores have allowed direct detection/monitoring of biomolecules in aqueous media and in live cells. In this review, key peptide-based approaches for different biological applications are presented. Keywords: fluorescent probe; fluorophores; molecular

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

• 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

• relevant peptide. In the case of RGD, the more pronounced differences between the UVRR spectra of the free and complexed GCI (1:1 mixture) clearly indicate a stronger binding of GCI to RGD compared with BA. A tentative assignment of the experimentally observed changes upon molecular recognition is based on

• strengths. Various spectroscopic techniques can be employed for monitoring these changes. For example, electronic absorption or fluorescence spectroscopy can probe the spectral differences due to the complexation of the supramolecular ligand with a peptide or protein. However, electronic spectroscopies

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• genomic information suggests the presence of biosynthetic genes for nonribosomal peptide synthetase and type III polyketide synthase in some Kocuria strains [18], which leaves a hope for new secondary metabolites. At present, only a few limited structural types of metabolites, including polyamine-derived

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

• of the N-terminal of the branch increased the stability of the branched peptides. Moreover, these branched peptides facilitate the delivery of the proteins into cells. This work contributes insights for the development of peptide supramolecular assemblies via enzymatic noncovalent synthesis in

• , peptide assemblies are being explored for a wide range of applications, including cell cultures [6], tissue engineering [7], drug delivery [8][9][10][11], antibacterial agents [12][13], regarding biomineralization [14][15], as collagen mimics [16], anisotropic hydrogels [17][18], for cancer therapy [19

• ][20][21][22][23][24][25][26], as mimicry of amyloids [27], in the context of intracellular phase transition [28], and in molecular imaging [29][30]. Most of these studies are centered on peptide amphiphiles or amphiphilic peptides that are linear in geometry. Nature, however, also produces and

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

• solution, potentially giving rise to highly selective receptors if the two binding sites are arranged at a distance that allows for binding a diphosphate, but not a larger triphosphate anion. The peptide and cyclopeptide-derived receptors introduced by Jolliffe are examples [26] along with a range of

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity

• Yuvixza Lizarme-Salas,
• Alexandra Daryl Ariawan,
• Ranjala Ratnayake,
• Hendrik Luesch,
• Angela Finch and
• Luke Hunter

Beilstein J. Org. Chem. 2020, 16, 2663–2670, doi:10.3762/bjoc.16.216

• advantage of improved aqueous solubility. The inhibition of BACE-1 was measured using a fluorogenic peptide substrate according to an established method (Figure 4b) [34]. Intriguingly, the relative activities of 1 vs 2 were reversed in comparison with the AChE assay. The lead compound 1 achieved the

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• be reserved for other future uses. To specify a glycopeptide, users may also inscribe them directly in the peptide using the existing branching rules: “PEP(AG(LY)CAN)TIDE” would describe a biantennary glycan bound to the threonine of a peptide. Because the number sign is used to indicate a

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• approach by investigating the in-silico binding of a peptide and glycopeptide epitope of the glycoprotein Mucin 1 (MUC1) binding with the antibody AR20.5. To study the binding, we performed molecular dynamics simulations using OpenMM and then used the Galaxy platform for data analysis. The same analysis

• analysis were carried out. These analyses were used to rapidly assess key features of the system, interrogate the dynamic structure of the ligand, and determine the role of glycosylation on the conformational equilibrium. The glycopeptide conformations in solution change relative to the peptide; thus a

• partially pre-structuring is seen prior to binding. Although the bound conformation of peptide and glycopeptide is similar, the glycopeptide fluctuates less and resides in specific conformers for more extended periods. This structural analysis which gives a high-level view of the features in the system

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

• the unsubstituted parent ligand [31][32]. These ligands bind KMe3 in a short histone 3 (H3) peptide tight enough to even displace natural methyl-lysine binding proteins such as plant homeodomain (PHD) containing epigenetic readers. Since the H3 peptides are synthetic and not easily available in

• isotope-labeled form, a competition experiment was set up with 15N-labeled PHD domains. First, the methylated histone peptide was titrated to the PHD domain, resulting in chemical shift perturbations. The calixarene ligand was subsequently titrated to the same sample now containing the binary PHD–histone

• complex. Competition of the ligand for the peptide resulted in release of unbound PHD domain, which is evident from the signals shifting back towards the position of the free protein in the absence of peptide. The Crowley lab has conducted multiple binding model studies comparing binding of sulfonato and

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• with Selectfluor® [153]. The authors justified the use of protecting groups due to their extensive use in peptide synthesis. Of all the PGs tested, phthalimide (Phth)- and trifluoroacetate (TFA)-protected substrates underwent photosensitized C–H fluorination to give the highest yield of 80% and 71% of

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• packages have been developed for analysis of outputs from MS technology to automate the process of transformation of raw MS data into ion intensities and matching them with appropriate glycan and peptide sequence databases for glycopeptide identification (reviewed in [12][13][14][15][16]). However, there

• perform quantification. Proteome Discoverer allows robust and facile measurement of peptide abundances using MS1 peptide area under the curve (AUC) information. We developed GlypNirO to integrate the outputs from Byonic and Proteome Discoverer to improve the efficiency, ease, and robustness of

• quantitative glycoproteomic data analysis. GlypNirO takes Byonic and Proteome Discover output files, and user-defined sample information and processing parameters, performs a series of automated data integration and computational steps, and provides informative and intuitive output files with site or peptide

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

• peptide chain and DNA/RNA interacting aromatic moiety, for instance peptide-based DNA/RNA-intercalators [1][2], as well as many DNA/RNA groove binding small molecules [3][4]. Inspired by these natural examples, the development of novel DNA/RNA targeting synthetic molecules has been in scientific focus for

• [9]). One of the approaches relies on amino acids conjugated with various DNA/RNA-binding chromophores, thereby yielding effective spectrometric sensing systems due to their interactions with DNA. In this approach, chromophores can be combined with peptide sequences in various ways, thus giving

• access to large libraries of close analogues. Further, in such peptide-based chromophore systems, a multitude of different chromophores/fluorophores [10] could allow fine tuning of spectroscopic responses to various DNA/RNA sequences. With this concept in mind, Piantanida and co-workers recently

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

• Goutam Ghosh Gustavo Fernandez Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Correnstraße 40, 48149 Münster, Germany 10.3762/bjoc.16.168 Abstract Peptide-based biopolymers represent highly promising biocompatible materials with multiple applications, such as tailored

• 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

• secondary structures, which lead to nanostructured materials [16][17]. Noncovalent interactions, such as hydrogen bonding, van der Waals interactions, hydrophobic interactions, electrostatic interactions, and π–π interactions [18][19][20][21][22] are common driving forces in peptide self-assembly. These

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

• ]. This binding model 10 can be applied to cell-surface GAGs to enhance the cellular uptake efficiency. The peptide 9, with rhodamine B attached, successfully enters into the living cells while the control peptide 11 with a simple guanidinium group shows a negligible uptake efficiency. In addition, the

• efficient delivery of a model protein (avidin, around 67 kDa) into cells through biotin–avidin technology could be achieved in the presence of this strikingly small peptide. However, the uptake of peptide 9-labeled avidin was dramatically reduced into cells that express less GAGs on the cell surfaces. These

• more stable complexes 12 with the phosphodiesters in the DNA backbone, and thus making it possible to transfect cells with shorter peptides. In 2015, the Schmuck group reported the first example of a small peptide with only four amino acids for gene transfection [27]. The binding affinity of 13 to DNA

Syntheses of spliceostatins and thailanstatins: a review

• William A. Donaldson

Beilstein J. Org. Chem. 2020, 16, 1991–2006, doi:10.3762/bjoc.16.166

• (Figure 1) are a family of linear peptide/polyketide natural products isolated from the bacteria Burkholderia sp. FERM BP-3421 [1][2][3] (originally identified as Pseudomonas sp. No 2663) and Burkholderia sp. MSMB 43 [4][5]. These compounds are of interest due to their ability to bind to a subunit of the