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

• noncovalent synthesis [41][42] in a cellular environment. Results and Discussion Molecular design We designed the branched peptides including the DEXXXLLI sequences [43] for this study. The DEXXXLLI (X is any amino acid) sequences are sorting signals of adaptor protein (AP) complexes, which play a critical

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

• regulate that amino acid sequences are written after “ ; ”, lipid moieties are written after “ : ”, and other glycosides are written after “ # ” (GR1). For example, a glucose β-linked to a Ceramide is written as “Gb:C.” Uncertainty rules describe syntax for when certain features of the SU are unknown or

• Krambeck et al. created, later researchers introduced new attributions that specify and simplify the description of reactions. Bennun et al. and Spahn et al. include the amino acid at the end of the Linear Code attached by a semicolon “ ; ”. This suffix is exactly the syntax from the original Linear Code

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

• the MUC1 VNTR domain. Thus, a synthetic 8-amino acid peptide (APDTRPAP) and the corresponding Tn glycopeptide were synthesized. It was found from the co-crystallization of the AR20.5 antigen-binding fragment (Fab) with the MUC1 peptide and glycopeptide that the glycan moiety of the glycopeptide did

• (physiological temperature). Missing amino acid residues were added. Energy minimization and MD (equilibration and production) simulations were performed using OpenMM [35] and the CHARMM36 force field [36] using the OpenCL platform with mixed precision. Equilibration and production dynamics were carried out as

• simulation. This is defined as the carbon–nitrogen distance between the first and last amino acid residues of the antigen. A time-series analysis provides some insight, while a histogram provides a clearer understanding of the most populated conformations (Figure 3). A Ramachandran plot [41] is a well-known

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

• formed between the charged head group of the encapsulated amino acid and one of the phosphate moieties attached to the tweezer’s central benzene ring [5]. Supramolecular tweezers have not only proven to be interesting tools to modulate protein–protein interactions [6][7], reverse amyloid fibril formation

• negatively charged sulfonate [20][21][22][24][25][27][28][29][30][31][32][34][36][37] or phosphonate [23][33][35] substituents, the aliphatic side chain of the amino acid lines the aromatic bowl-like structure of the calixarene, while the positively charged end group being situated between the sulfonate or

• 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

Palladium nanoparticles supported on chitin-based nanomaterials as heterogeneous catalysts for the Heck coupling reaction

• Tony Jin,
• Malickah Hicks,
• Davis Kurdyla,
• Sabahudin Hrapovic,
• Edmond Lam and
• Audrey Moores

Beilstein J. Org. Chem. 2020, 16, 2477–2483, doi:10.3762/bjoc.16.201

• transformations [7][8][9]. Furthermore, the chiral nature of polysaccharides has also been used as a tool for enantioselective catalysis such as carbonyl hydrogenations and amino acid hydrolysis, proving the unique ability of these biomass-based supports [10][11]. Chitin is another type of biomass feedstock that

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• ://beta.glyco.me/sugarbuilder) is online software for drawing glycans. The interface leads to rapid carbohydrate construction. A panel of monosaccharide templates complements the drawing interface (one pre-built oligosaccharide is available (Figure 8, top). The user can start a chain from amino acid residues: Asn

Recent developments in enantioselective photocatalysis

• Callum Prentice,
• James Morrisson,
• Andrew D. Smith and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2020, 16, 2363–2441, doi:10.3762/bjoc.16.197

• tautomer 147, and the CPA-catalysed Povarov reaction between them gives the enantioenriched THQ 144 in good yields and enantioselectivities (4 examples, up to 97:3 er). This reactivity has been extended to enamides 148, with the imine generated from the α-amino acid 149 now reacting with 148 in a CPA

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

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

• -glycosylation; O-glycosylation; Python; Introduction Glycosylation is a key post-translational modification critical for protein folding and function in eukaryotes [1][2][3]. Diverse types of glycosylation are known, all involving modification of specific amino acid residues with complex carbohydrate

• modification. The script therefore calculated the theoretical mass of the glycan from the Glycans NHFAGNa column, and matched this to the corresponding amino acid in the peptide. This allowed the unambiguous assignment of each site of glycosylation from the Byonic output. Options were provided to either

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• the links between glycans’ sequence and the 3D structure. This direct relationship is a well-recognized and broadly accepted concept in proteins’ structural biology, according to which the amino acid sequence dictates the functional 3D fold and its stability. However, the same notion is not generally

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

• Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany 10.3762/bjoc.16.170 Abstract Two novel unnatural amino acids, prepared by linking a dicationic purple-coloured and fluorescent naphthalene diimide (NDI) at core position to amino acid side chains of variable length, strongly

• interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520–540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid–NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U

• )-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on

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

• ], the ease of materials preparation, and the versatility in tuning their secondary structures (e.g., β-sheet and α-helix) by designing the amino acid sequence [15]. Peptidomimetic foldamers designed from nonnatural amino acid sequences are also well characterized systems due to their propensity to form

• ], peptic ulcer [48], asthma [49], cardiovascular diseases [50], and hypertension [51]. A particularly important aspect of peptides that contain both hydrophobic and hydrophilic amino acid residues is their amphiphilicity, which plays a crucial role in the self-assembly process [52]. Keeping these factors

• nanostructures as well as the secondary structures. Results and Discussion Solid-phase peptide synthesis and purification The target octapeptide was synthesized in the solid phase following four steps, including: i) deprotection of the Fmoc protecting group, ii) coupling of an amino acid, iii) cleavage of the

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• the interplay between the substituents and the main chain groups of the amino acid residue. This study aims to showcase the polarity-related effects that arise from the interaction between the functional groups in molecular models. Properties such as conformation, acid–base transition, and amide-bond

• structure of alanine, which constitute the backbone features. The classification of the amino acid residues by hydrophobic/hydrophilic usually refers to the variable part, which locates in the side chain. The introduction of an aliphatic or an aromatic group into the side chain usually renders an amino acid

• chemically inert under most biologically relevant conditions. The presence of these groups adjacent to the proline structure helps to modulate the conformational landscape of the parent amino acid, and this effectively alters the folding of the peptide chain when an analogue is included in it as a residue

When metal-catalyzed C–H functionalization meets visible-light photocatalysis

• Lucas Guillemard and
• Joanna Wencel-Delord

Beilstein J. Org. Chem. 2020, 16, 1754–1804, doi:10.3762/bjoc.16.147

• azoles. His research group discovered that the abundant and inexpensive CuI catalyst allowed the direct arylation of benzoxazoles under UV-photoactivation (Figure 46) [106]. Remarkably, this totally site-selective photoinduced C–H arylation took place at room temperature and the use of amino acid ligands

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

• , carboxyl groups, amides, amino acid side chains), our DCL should be applicable to a similar scope. In order to show that our system offers a general approach to find binders for biomolecules in water we choose to test our DCL against peptide templates. Results and Discussion We started from our established

• CXC peptide building block design (single-letter code) were the terminal amino acids are cysteine (C) and the X can be any amino acid (Scheme 1a). This allows for rapid synthesis of various new building bocks by standard Fmoc based SPPS using Trt protecting groups for cysteine, which are subsequently

• of tripeptide dimers are formed after oxidation. a) Synthesis of the parallel and antiparallel isomers p(CFC)2 and a(CFC)2. b) Templates FF. YY and AA. c) Dipeptides FA, AF and amino acid F used for comparison. Binding behavior of several peptides (30 mM) towards p(CFC)2 and a(CFC)2 (1.5 mM

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

Photocatalyzed syntheses of phenanthrenes and their aza-analogues. A review

• Alessandra Del Tito,
• Havall Othman Abdulla,
• Davide Ravelli,
• Stefano Protti and
• Maurizio Fagnoni

Beilstein J. Org. Chem. 2020, 16, 1476–1488, doi:10.3762/bjoc.16.123

• biaryls 5.1a–d in up to excellent yields at room temperature by using α-bromoesters as radical precursors and [fac-Ir(ppy)3] as the photoredox catalyst [49]. A similar photocatalyzed tandem insertion/cyclization approach based on isocyanides and amino acid/peptide-derived Katritzky salts as precursors of

[3 + 2] Cycloaddition with photogenerated azomethine ylides in β-cyclodextrin

• Margareta Sohora,
• Leo Mandić and
• Nikola Basarić

Beilstein J. Org. Chem. 2020, 16, 1296–1304, doi:10.3762/bjoc.16.110

• involves condensation of phthalic anhydride with unprotected amino acid. The synthetic procedures and characterization of compounds are reported in Supporting Information File 1. Irradiation of 1 was conducted first in CH3CN in the presence of AN, with or without addition of H2O (Table 1). Phthalimide 1

Synthesis of pyrrolidinedione-fused hexahydropyrrolo[2,1-a]isoquinolines via three-component [3 + 2] cycloaddition followed by one-pot N-allylation and intramolecular Heck reactions

• Xiaoming Ma,
• Suzhi Meng,
• Xiaofeng Zhang,
• Qiang Zhang,
• Shenghu Yan,
• Yue Zhang and
• Wei Zhang

Beilstein J. Org. Chem. 2020, 16, 1225–1233, doi:10.3762/bjoc.16.106

• reactions to make it a green synthetic method with pot, atom and step economy (PASE) [55][56]. Results and Discussion Following the reported procedures for amino ester- and amino acid-based [3 + 2] cycloaddition reactions, pyrrolidine adducts 5 and 6 were synthesized by a three-component reaction of 1 or 2

A cyclopeptide and three oligomycin-class polyketides produced by an underexplored actinomycete of the genus Pseudosporangium

• Shun Saito,
• Kota Atsumi,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Naoya Oku,
• Md. Rokon Ul Karim,
• Hisayuki Komaki and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1100–1110, doi:10.3762/bjoc.16.97

• elucidated the presence of three amino acid residues, N-acetyltyrosine (AcTyr), proline (Pro), and tryptophane (Trp) (Figure 2). HMBC correlations from H-2' and H-3' to C-4' and from H-4' and H-5' to C-3' joined two COSY-defined fragments, H-2'/H-3' and H-4'/H-5'. Further HMBC correlations from H-2' to C-5

• linear gradient of MeCN from 15% to 85% over 30 min. Retention times for the amino acid standards were 20.1 min for ʟ-Pro-ʟ-FDLA, 21.1 min for ᴅ-Pro-ʟ-FDLA, while the ʟ-FDLA-hydrolysate of 1 gave a peak at 20.1 min (Figure S8 in Supporting Information File 1). (R)- and (S)-PGME amides of 1 (5a and 5b) To

Fluorinated phenylalanines: synthesis and pharmaceutical applications

• Laila F. Awad and
• Mohammed Salah Ayoup

Beilstein J. Org. Chem. 2020, 16, 1022–1050, doi:10.3762/bjoc.16.91

• membrane permeability and reactivity [11][12][13][14]. The effect of peptide structure and stability has been found to depend on the position and number of fluorine atoms within the amino acid chains [15][16][17]. Incorporation of fluorinated aromatic amino acids into proteins can increase their shelf life

• -tetrafluorocyclohexylphenyliodide 4 and 5 were subjected to Jackson’s methodology for the synthesis of the appropriate amino acid products. Thus, the coupling of the zinc homoenolate of (R)-iodoalanine 2 with a mixture of 4 and 5 in the presence of Pd(dba)3 and SPhos resulted in an excellent conversion to the fully protected amino

• with zincate 11 using a variety of catalysts and different reaction conditions, was unsuccessful. However, coupling of 4-[bis(dimethoxybenzyl)difluoromethyl]benzyl bromide (14) with the lithium enolate of William`s lactone 15 gave the protected amino acid 16 in 80% yield. The desired protected amino

Fabclavine diversity in Xenorhabdus bacteria

• Sebastian L. Wenski,
• Harun Cimen,
• Natalie Berghaus,
• Sebastian W. Fuchs,
• Selcuk Hazir and
• Helge B. Bode

Beilstein J. Org. Chem. 2020, 16, 956–965, doi:10.3762/bjoc.16.84

•  1). Here, the polyamine was connected by one or two polyketide units to a NRPS part, with His in the second (Table 1, R1) and Pro or Val in the sixth amino acid position (Table 1, R2/R3 and Figure S18, Supporting Information File 1), leading to the smallest set of identified derivatives (11–14). In

• X. szentirmaii, derivatives with an Ala incorporated at the second amino acid position were identified (15 and 16, Table 1, R1) in addition to the already described derivatives 17–22. However, the derivatives featuring the described Ala incorporation were not detected in any other strain analyzed

• (Table 1 and Figure S2, Supporting Information File 1) [20]. Furthermore, besides the dominant derivatives with a Val or Thr residue in the sixth amino acid position (Table 1, R2/R3), derivatives containing Pro were also observed, but with a much lower signal intensity (Figure S3, Supporting Information

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

• mechanisms of the interaction of glycopeptides with the cell surface [16]. Our focus lay on the preparation of glycopeptide libraries containing ʟ-asparagine since many saccharides on the cell surface are N-glycosidically linked to this amino acid [8]. The most abundant sugars found in these asparagine

• Table 1, the yields for all condensations with HBTU and HATU are in a comparable range. Only for the cellobiosyl Asp amino acid 3f (Table 1, entry 6), the lactosylated Asp–Phe–Ala tripeptide 6e (Table 1, entry 23), and the galactosylated Asp–Trp dipeptide 5b (Table 1, entry 14), HATU gave a

Copper catalysis with redox-active ligands

• Agnideep Das,
• Yufeng Ren,
• Cheriehan Hessin and
• Marine Desage-El Murr

Beilstein J. Org. Chem. 2020, 16, 858–870, doi:10.3762/bjoc.16.77

• scaffolds such as gem-disubstituted (21k) and trisubstituted (21i and 21n,o) aziridines (Scheme 11). Furthermore, the reaction conditions are compatible with aldehyde, ester or ketone functions. Metalloenzymes routinely rely on 3d metals and amino acid-derived coordination spheres to perform complex (multi

Synthesis and herbicidal activities of aryloxyacetic acid derivatives as HPPD inhibitors

• Man-Man Wang,
• Hao Huang,
• Lei Shu,
• Jian-Min Liu,
• Jian-Qiu Zhang,
• Yi-Le Yan and
• Da-Yong Zhang

Beilstein J. Org. Chem. 2020, 16, 233–247, doi:10.3762/bjoc.16.25

• catalytic mechanism for this process is shown in Scheme 1 [2][3][4][5][6]. The HPPD amino acid sequence homologies in plants and mammals are significantly different [7][8], and this difference affects the binding stability between an inhibitor and HPPD, leading to inhibitor activities that differ among