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

• 13.8) [1] replicating the side-on salt-bridge binding interaction made between the guanidinium functionality of arginine and an aspartic acid residue in the protein. Consequently, this moiety has been used in various integrin inhibitors (Figure 1) [2][3][4][5][6][7][8]. Current routes to install

Synthesis of new dihydroberberine and tetrahydroberberine analogues and evaluation of their antiproliferative activity on NCI-H1975 cells

• Giacomo Mari,
• Lucia De Crescentini,
• Serena Benedetti,
• Francesco Palma,
• Stefania Santeusanio and
• Fabio Mantellini

Beilstein J. Org. Chem. 2020, 16, 1606–1616, doi:10.3762/bjoc.16.133

• effects [32], inhibits both hERG current and the expression of hERG protein [33], inhibits the pancreatic lipase [34], shows antiradical, revitalizing and antifibrotic properties for dermatological applications [35], manifests a synergic effect with antibiotics [36], and displays antitumoral activities

• proliferation as evaluated by SRB assay (estimating total protein content) at 24 h and 48 h of treatment. Data are expressed as mean ± SD (n = 3). *p < 0.05 vs CTR (DMSO 0.05%). Preparation of functionalized-BER, -DHBER and -THBER derivatives. Substrate scope of hydrazono-DHBER. Reaction conditions: DHBER (1.0

Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida)

• Cora Hertzer,
• Stefan Kehraus,
• Nils Böhringer,
• Fontje Kaligis,
• Robert Bara,
• Dirk Erpenbeck,
• Gert Wörheide,
• Till F. Schäberle,
• Heike Wägele and
• Gabriele M. König

Beilstein J. Org. Chem. 2020, 16, 1596–1605, doi:10.3762/bjoc.16.132

• were shown to share and cover various core functions of sponge metabolism by functionally equivalent symbionts, analogous enzymes, or biosynthetic pathways [16][79][80]. Another Spongia species, S. officinalis, was shown to harbour bacteria with terpenoid cyclases/protein prenyltransferases responsible

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

Synthesis of new fluorescent molecules having an aggregation-induced emission property derived from 4-fluoroisoxazoles

• Kazuyuki Sato,
• Akira Kawasaki,
• Yukiko Karuo,
• Atsushi Tarui,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2020, 16, 1411–1417, doi:10.3762/bjoc.16.117

• bioprobes [9][10][11][12][13][14]. For example, it is presumed that prion disease, which is caused by the accumulation of prion protein aggregates in the brain, plays an important role in the pathophysiological mechanism of prion protein-polymerized oligomers. However, since prion protein oligomers cannot

Synthesis, antiinflammatory activity, and molecular docking studies of bisphosphonic esters as potential MMP-8 and MMP-9 inhibitors

• Abimelek Cortes-Pacheco,
• María Adelina Jiménez-Arellanes,
• Francisco José Palacios-Can,
• José Antonio Valcarcel-Gamiño,
• Rodrigo Said Razo-Hernández,
• María del Carmen Juárez-Vázquez,
• Adolfo López-Torres and
• Oscar Abelardo Ramírez-Marroquín

Beilstein J. Org. Chem. 2020, 16, 1277–1287, doi:10.3762/bjoc.16.108

• was pointing away from the zinc ion [39]. The calculated distances from the Zn2+ ion and the different sites at the ligand and the protein are summarized in Table 5. The zinc chelation in MMP-9 occurred in a different way. The predicted orientation of the histidine residues at the catalytic site were

• not aiming directly at the metal ion. However, it can be assumed that because of the flexibility of the protein in solution, the coordination to the metal ion would be possible. The targets 3 and 4 could coordinate the Zn2+ ion through the oxygen atom double bonded to the phosphorus atom (P=O) of one

• molecules inside the catalytic site allowed the coordination through the ester groups rather than through the phosphonate moieties. The calculated distances from the Zn2+ ion and the different sites at the ligand and the protein are summarized in Table 6. In Figure 4, a schematic representation of the

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• researchers, The Worm Breeder’s Gazette, which combines advice and suggestions on methods with informal communication of new findings in advance of publication. For example, the Nobel prize-winning use of a green fluorescence protein as a marker was reported in the Gazette by Martin Chalfie and colleagues

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

• currently described 18 alternative splice variants of AR mRNA – AR-FL, AR45, AR-23, AR V1-V14 and AR-8. Most of them encode small-sized or functionally inactive proteins [16]. However, all translated isoforms of the AR protein contain NTD, which is critical for AR function. This is the main reason to target

Synthesis of esters of diaminotruxillic bis-amino acids by Pd-mediated photocycloaddition of analogs of the Kaede protein chromophore

• Esteban P. Urriolabeitia,
• Pablo Sánchez,
• Alexandra Pop,
• Cristian Silvestru,
• Eduardo Laga,
• Ana I. Jiménez and
• Carlos Cativiela

Beilstein J. Org. Chem. 2020, 16, 1111–1123, doi:10.3762/bjoc.16.98

• complexes 4. Treatment of 4 with CO in a MeOH/NCMe mixture promoted the methoxycarbonylation of the palladated carbon and the release of the corresponding ortho-functionalized 1,3-diaminotruxillic bis-amino esters 5 as single isomers. Keywords: amino acids; C–H activation; Kaede protein; oxazolones

• precursors of the photoconvertible chromophore of the Kaede protein, an imidazolone with outstanding photophysical properties [31][32][33][34][35][36][37][38]. It is clear from Figure 2b that the molecular skeleton contains different reactive functional groups, which offer a variety of structural

• findings were also confirmed by analysis of the 13C NMR spectra. Conclusion The synthesis of cyclobutane 1,3-diaminotruxillic bis-amino acids has been achieved with full stereoselectivity (ε-isomer) starting from polyfunctional oxazolones 2 derived from the chromophore of the Kaede protein in three steps

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

• consisting of glucose 0.5%, glycerol 2%, soluble starch 2%, Pharmamedia (Traders Protein) 1.5%, dry yeast (Kamaishi Hamayuri Yeast, Nihon Tensai Seito Co., Ltd.) 0.3%. The pH of the medium was adjusted to 7.0 before sterilization. The inoculated flasks were placed on a rotary shaker TB98 (Takasaki Scientific

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

• the properties of peptides and proteins [5][6][7], influencing aspects such as protein folding, protein–protein interactions, ribosomal translation, lipophilicity, acidity/basicity, optimal pH, stability, thermal stability, and therapeutic properties [8][9][10]. This extends to metabolic properties of

• , especially in therapeutic proteins and peptide-based vaccines [18]. Enhanced catabolic stability [6] can arise from the role of particular aromatic amino acids in membrane–protein interactions [19]. Furthermore, fluorinated aromatic amino acids can alter enzymatic activity as a result of enhanced protein

• protein–protein and protein–ligand interactions and consequently metabolic processes [20][21]. Fluorinated phenylalanines (FPhe) have been incorporated into various proteins and enzymes [22][23][24][25] with advantageous biophysical, chemical, and biological properties, and their effect on the stability

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

• fcl BGCs in Xenorhabdus and Photorhabdus strains, several candidate clusters were identified, which were conserved both in their BGC synteny as well as at the single protein level (Figure 2) [22]. The strain KK7.4 showed protein identities of ≥95% with X. stockiae and strain KJ12.1 (Figure S1

• originally also contained the NRPS-PKS-hybrid genes (Figure 2) [22]. In contrast, the BGC of P. temperata is reduced to only harbor the homologous genes of fclC, fclD and fclE (Figure 2) [22]. X. innexi also harbors a fcl-like BGC, with protein identities of 68–90% compared to X. stockiae (Figure S1

Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition

• Sivaraman Balasubramaniam,
• Sajith Vijayan,
• Liam V. Goldman,
• Xavier A. May,
• Kyra Dodson,
• Sweta Adhikari,
• Fatima Rivas,
• Davita L. Watkins and
• Shana V. Stoddard

Beilstein J. Org. Chem. 2020, 16, 628–637, doi:10.3762/bjoc.16.59

• involve acetylation/deacetylation of histone proteins by histone deacetylases (HDACs) [1]. HDACs belong to an important family of enzymes consisting of 18 isozymes. They control protein acetylation, which is a change that occurs after translation. In addition, they regulate gene transcription, cell

• Biotek Synergy HTX multimodal plate reader after incubation for 30 minutes. Preparation of the HDAC8 receptor for docking The HDAC8 crystal structure (protein database pdb: 1W22) [32] was utilized as the docking receptor for all compounds. This receptor is crystalized as a dimer thus only the A chain was

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54

• “D“ where a bioactivity “A” with a quantitative result “R” (e.g., an IC50) is reported for chemical structure “C” that modulates (e.g., inhibits) a protein target “P”. A useful shorthand for this connectivity thus becomes DARCP. The problem at the core of this article is that the community has spent

• . However, we will need to await the technical applicability in respect to DARCP capture to see if this opens up connectivity. Keywords: activity data; databases; drug discovery; chemical structures; protein targets; Introduction This article assesses a key aspect of data sharing that has the potential to

• Google and indexed for chemistry searching [4][5]. Structures: A necessary focus of this article will be traditional small-molecule chemistry that is not too far outside the rule-of-five lead-like property space. In terms of connectivity antibodies, other protein biotherapeutics, as well as large

A systematic review on silica-, carbon-, and magnetic materials-supported copper species as efficient heterogeneous nanocatalysts in “click” reactions

• Pezhman Shiri and
• Jasem Aboonajmi

Beilstein J. Org. Chem. 2020, 16, 551–586, doi:10.3762/bjoc.16.52

Two antibacterial and PPARα/γ-agonistic unsaturated keto fatty acids from a coral-associated actinomycete of the genus Micrococcus

• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku,
• Nobuyasu Matsuura,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 297–304, doi:10.3762/bjoc.16.29

• incubated at 30 °C on a rotary shaker at 200 rpm for two days. Three mL each of the seed culture were inoculated into 29 500 mL K-1 flasks containing 100 mL of A16 production medium, which consisted of glucose 2%, Pharmamedia (Traders Protein, Memphis, TN, USA) 1%, CaCO3 0.5%, Diaion HP-20 (Mitsubishi

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

• balance of the plant, which interrupts nucleic-acid and protein metabolism, and is especially effective in broadleaf weeds, such as Amaranthus retroflexus and Alfalfa. The application of 2,4-D causes excessive growth that ultimately results in plant death. Consequently, 2,4-D has become one of the world’s

• docking study was conducted with the method reported previously [10][19][32][33][34]. Crystal structures of Arabidopsis thaliana HPPD (PDB ID: 1TFZ) with the native ligand, named DAS869 were downloaded from the Protein Data Bank. The docking was carried out using Discovery Studio 4.0. During the docking

• process, all water molecules were removed. The ligand and protein were prepared with the Dock Ligands tool before docking. By using Define and Edit Binding Site tool to identify the active site. Then the center of the native ligand was deleted. Utilizing the CDOCKER, the prepared ligand was docked into

Combination of multicomponent KA² and Pauson–Khand reactions: short synthesis of spirocyclic pyrrolocyclopentenones

• Riccardo Innocenti,
• Elena Lenci,
• Gloria Menchi and
• Andrea Trabocchi

Beilstein J. Org. Chem. 2020, 16, 200–211, doi:10.3762/bjoc.16.23

• molecular scaffolds to develop chemical libraries can increase the chance of finding compounds able to address the so-called “undruggable” targets, such as protein–protein interactions [1]. In this context, molecules containing one or more rings are of primary interest, as they will suffer a reduced

• conformational entropy penalty upon binding to a protein target, and the approach of constraining the ligand conformation with a ring is widely used in drug design [2]. Accordingly, with increasing interest for sp3-rich molecules, spirocyclic compounds are being considered valuable as molecular platforms for the

• generation of high-quality small molecule collections, taking advantage of the stereochemical diversity, and of their three-dimensional shape and structural bias to develop lead compounds, specifically in the field of protein–protein interactions [3][4][5][6]. Spiranic rings such as spiroketals are present

Potent hemithioindigo-based antimitotics photocontrol the microtubule cytoskeleton in cellulo

• Alexander Sailer,
• Franziska Ermer,
• Yvonne Kraus,
• Rebekkah Bingham,
• Ferdinand H. Lutter,
• Julia Ahlfeld and
• Oliver Thorn-Seshold

Beilstein J. Org. Chem. 2020, 16, 125–134, doi:10.3762/bjoc.16.14

• addressable by photopharmacology. Keywords: antimitotics; cytoskeleton; hemithioindigo; photopharmacology; photoswitch; Introduction The cytoskeletal scaffolding protein tubulin, a heterodimer consisting of α and β subunits, each of various isotypes, reversibly assembles into giant non-covalent polymeric

• applied, photopharmacology has drawn great interest for studies of crucial biological processes in a range of fields, from neuroscience [5][6] and G-protein-coupled receptor (GPCR) function [7][8] to antibiotic research [9]. Particularly in the context of MT biology, photopharmacology is an attractive

• heterostilbenes that deliver green fluorescent protein (GFP)-orthogonal MT photocontrol [17]. However, in both azobenzene and heterostilbene scaffolds, the steric properties of the E- and Z-isomer are so different that the protein binding site shape determines that the Z-isomer (the lit-form) is the more

Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides

• Sabrina Müller,
• Jannik Paulus,
• Jochen Mattay,
• Heiko Ihmels,
• Veronica I. Dodero and
• Norbert Sewald

Beilstein J. Org. Chem. 2020, 16, 60–70, doi:10.3762/bjoc.16.8

• compounds have frequently been employed as modules, e.g., to control protein–DNA interactions. However, their use in conjunction with minor groove-binding imidazole/pyrrole (Im/Py) polyamides is yet unprecedented. Dervan-type Im/Py polyamides were equipped with an azobenzene unit, i.e., 3-(3-(aminomethyl

Synthesis and characterization of bis(4-amino-2-bromo-6-methoxy)azobenzene derivatives

• David Martínez-López,
• Amirhossein Babalhavaeji,
• Diego Sampedro and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2019, 15, 3000–3008, doi:10.3762/bjoc.15.296

• isomerization cycles [10]. Efforts to apply 1 to photocontrol protein–protein interactions have recently been reported [13]. Despite the usefulness of 1 as a photoswitch, compounds undergoing photoisomerization at longer wavelengths (>700 nm) would be valuable since the penetration of light through tissue is

Two new aromatic polyketides from a sponge-derived Fusarium

• Mada Triandala Sibero,
• Tao Zhou,
• Keisuke Fukaya,
• Daisuke Urabe,
• Ocky K. Karna Radjasa,
• Agus Sabdono,
• Agus Trianto and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2019, 15, 2941–2947, doi:10.3762/bjoc.15.289

• % yeast extract, 1.5% Pharmamedia (Traders Protein), and 1% Diaion HP-20 (Mitsubishi Chemical Co.). The inoculated flasks were placed on a rotary shaker (200 rpm) at 30 °C for 7 days. Extraction and isolation Extraction and isolation of secondary metabolites from strain KJMT.FP.4.3 were carried out in a

Chemical synthesis of tripeptide thioesters for the biotechnological incorporation into the myxobacterial secondary metabolite argyrin via mutasynthesis

• David C. B. Siebert,
• Roman Sommer,
• Domen Pogorevc,
• Michael Hoffmann,
• Silke C. Wenzel,
• Rolf Müller and
• Alexander Titz

Beilstein J. Org. Chem. 2019, 15, 2922–2929, doi:10.3762/bjoc.15.286

• phosphopantetheinyl arm of the peptide carrier protein (CP). Analysis of mutasynthon 14 obtained via the convergent synthetic route by HPLC on a HILIC stationary phase and UV detection (A) and mass spectrometry (B). Synthesis of tripeptide thioesters. Reagents and conditions: (a) SOCl2, EtOH, 78 °C; (b) IBCF, NMM

Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering

• Eric J. N. Helfrich,
• Geng-Min Lin,
• Christopher A. Voigt and
• Jon Clardy

Beilstein J. Org. Chem. 2019, 15, 2889–2906, doi:10.3762/bjoc.15.283

• cyclization reactions. Textbook TCs are categorized into two classes and differ in their mechanisms of substrate activation as well as their protein folds [37][50][51][52]. Type I TCs trigger the formation of highly reactive allylic cations by heterolytic cleavage of the terminal pyrophosphate of farnesyl

• ) Terpene biosynthesis. LG: leaving group, black ball: acyl carrier protein. Abundance and distribution of bacterial terpene biosynthetic gene clusters as determined by genome mining (black) compared to experimentally characterized bacterial terpene BGCs (red). Terpenoid biosynthesis. Terpenoid biosynthesis

Emission and biosynthesis of volatile terpenoids from the plasmodial slime mold Physarum polycephalum

• Xinlu Chen,
• Tobias G. Köllner,
• Wangdan Xiong,
• Guo Wei and
• Feng Chen

Beilstein J. Org. Chem. 2019, 15, 2872–2880, doi:10.3762/bjoc.15.281

• To determine whether PpolyTPS genes encode functional terpene synthases, full-length cDNAs were amplified by RT-PCR and cloned into the protein expression vector pEXP-5-CT/TOPO. Recombinant PpolyTPSs were heterologously expressed in Escherichia coli and then tested for terpene synthase activities

• (Supporting Information File 1, Figure S2). Relatedness of PpolyTPSs to the TPSs from dictyostelid social amoebae, fungi, and bacteria When individual PpolyTPS genes were used as query to search against the nonredundant protein database at NCBI, the top hits for PpolyTPS2 and PpolyTPS3 were all from bacteria

• the Physarum polycephalum Genome Resources database (http://www.physarum-blast.ovgu.de). Protein sequences were predicated using TransDecoder (5.0.2) [37]. Putative terpene genes were searched against SmMTPSLs HMM profile [38] using HMMER 3.0 hmmsearch [39] with an E-value of 1e−5. The coding region