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

• O-glycan on fibrinogen alpha chain G272GSTSYGTGSETESPR (Figure 5a). HCC patients showed a relative decrease in disialylated and an increase in monosialylated O-glycan abundance on both plasma protease C1 inhibitor V45AATVISK and histidine-rich glycoprotein S271STTKPPFKPHGSR (Figure 5b and 5c

• G272GSTSYGTGSETESPR, (b) plasma protease C1 inhibitor V45AATVISK, and (c) histidine-rich glycoprotein S271STTKPPFKPHGSR. N = 3; values show mean; error bars show standard error of the mean; *, P < 0.05. Supporting Information Supporting Information File 548: Supplementary Tables S1–S42. Supporting Information File

Azo-dimethylaminopyridine-functionalized Ni(II)-porphyrin as a photoswitchable nucleophilic catalyst

• Jannis Ludwig,
• Julian Helberg,
• Hendrik Zipse and
• Rainer Herges

Beilstein J. Org. Chem. 2020, 16, 2119–2126, doi:10.3762/bjoc.16.179

• the Henry reaction, the nitroethane anion intermediate, coordinates to the Ni-porphyrin, which slows down nucleophilic addition to the nitrobenzaldehyde. Hence, the switchable catalyst 1 contains both, a catalytic center (nitrogen lone pair) and an inhibitor (Ni2+ ion). If the nitrogen lone pair

Convenient access to pyrrolidin-3-ylphosphonic acids and tetrahydro-2H-pyran-3-ylphosphonates with multiple contiguous stereocenters from nonracemic adducts of a Ni(II)-catalyzed Michael reaction

• Alexander N. Reznikov,
• Dmitry S. Nikerov,
• Anastasiya E. Sibiryakova,
• Victor B. Rybakov,
• Evgeniy V. Golovin and
• Yuri N. Klimochkin

Beilstein J. Org. Chem. 2020, 16, 2073–2079, doi:10.3762/bjoc.16.174

• ; tetrahydropyranes; Introduction Сhiral phosphonates [1][2] and phosphoryl-substituted heterocycles [2][3][4] have received significant attention in recent years due to their wide range of biological activity. For example, SF-2312 (1) is a natural antibiotic – an enolase inhibitor produced by the actinomycete

Synthesis of monophosphorylated lipid A precursors using 2-naphthylmethyl ether as a protecting group

• Jundi Xue,
• Ziyi Han,
• Gen Li,
• Khalisha A. Emmanuel,
• Cynthia L. McManus,
• Qiang Sui,
• Dongmian Ge,
• Qi Gao and
• Li Cai

Beilstein J. Org. Chem. 2020, 16, 1955–1962, doi:10.3762/bjoc.16.162

• ]. While the research suggested chemically pure lipid X had no immunostimulatory properties of lipid A, it did behave as a competitive inhibitor of LPS [13]. In this paper we describe a synthesis of lipid X (1) and the disaccharide lipid A precursor 2 (2,2′-N;3,3′-O-tetra[(R)-3-hydroxytetradecanoyl]-β(1→6

Selective preparation of tetrasubstituted fluoroalkenes by fluorine-directed oxetane ring-opening reactions

• Clément Q. Fontenelle,
• Thibault Thierry,
• Romain Laporte,
• Emmanuel Pfund and
• Thierry Lequeux

Beilstein J. Org. Chem. 2020, 16, 1936–1946, doi:10.3762/bjoc.16.160

• antiviral agents, respectively (Figure 1) [5][6]. The field of acyclonucleotides (ACN) has been explored less, however, the introduction of fluorine atoms showed remarkable effects. The most representative examples are phosphate analogues such as the nucleoside phosphorylase inhibitor III and acyclic

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• between 0.332–3.85 mM were established by a spectrophotometric assay with a purified recombinant GlfT2 enzyme, UDP-Galf as a donor substrate and analogs of the acceptor substrate [24][25][26][27][28][29][30]. The best reported IC50 value (0.180 mM) for a putative GlfT2 inhibitor was obtained for a

• synthesis of lipid-linked galactan. However, the experiments evaluating the dose effects of the predicted best (1bα) and the worst (3a) inhibitor on the mycobacterial galactan synthesis indicated the possibility of GlfT2 inhibition by 1bα at the highest tested concentration (10 mM). However, it is clear

Microwave-assisted efficient one-pot synthesis of N²-(tetrazol-5-yl)-6-aryl/heteroaryl-5,6-dihydro-1,3,5-triazine-2,4-diamines

• Moustafa Sherief Moustafa,
• Ramadan Ahmed Mekheimer,
• Saleh Mohammed Al-Mousawi,
• Mohamed Abd-Elmonem,
• Hesham El-Zorba,
• Afaf Mohamed Abdel Hameed,
• Tahany Mahmoud Mohamed and
• Kamal Usef Sadek

Beilstein J. Org. Chem. 2020, 16, 1706–1712, doi:10.3762/bjoc.16.142

• [2], antitumor [3], anti-HIV [4], inhibitor of Trypanosoma brucei [5], angiogenesis inhibitor [6], antiplasmodial antifolates [7], and antimicrobial [8]. Moreover, and in particular N2,6-disubstituted-1,3,5-triazine-2,4-diamines possess a wide range of chemotherapeutic activities [8][9][10][11

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

• canadine, is an isoquinoline alkaloid recurring in several plant species [55][56][57]. THBER is able to act to the central nervous system as an inhibitor [58], possesses hepatoprotective effects [59], is employed in the protection against cerebral ischemia-reperfusion injury [60], and shows anti-arrhythmic

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

• topoisomerase 1 inhibitor [14] and DNA intercalator), bicolorine (5-methyl-[1,3]dioxolo[4,5-j]phenanthridin-5-ium ion, a trypanocidal) [15], and the antimalarian nitidine, as well as ethidium bromide (EB), that has been employed as a DNA- and RNA-fluorescent marker for a long time (some examples are collected

One-step route to tricyclic fused 1,2,3,4-tetrahydroisoquinoline systems via the Castagnoli–Cushman protocol

• Aleksandar Pashev,
• Nikola Burdzhiev and
• Elena Stanoeva

Beilstein J. Org. Chem. 2020, 16, 1456–1464, doi:10.3762/bjoc.16.121

• IV inhibitor carmegliptin (2, DPP IV) with potential for the treatment of type-II diabetes [3][4]. A comparative study on novel classes of anticancer drugs identified benzo[a]quinolizines 3 and 4 (Figure 1) to be useful for a specific inhibition of heat shock response in cancer cells, which strongly

Recent synthesis of thietanes

• Jiaxi Xu

Beilstein J. Org. Chem. 2020, 16, 1357–1410, doi:10.3762/bjoc.16.116

• as inhibitor of kinases, insecticides, and acaricides, its sulfur analogue, 6-amino-2-thiaspiro[3,3]heptane (28) was prepared from the cheap starting material 2,2-bis(bromomethyl)propane-1,3-diol (11). Compound 11 was converted into 3-(tert-butoxycarbonyl)-1,1-bis(hydroxymethyl)aminocyclobutane (25

• -bis(hydroxymethyl)indolin-2-one (51) was reacted first with mesyl chloride and then treated with sodium sulfide to afford 6-bromospiro[indoline-3,3′-thietan]-2-one (53), which was further converted into the target inhibitor candidate 54 [42] (Scheme 12). 2-Methylene-γ-butyrolactone (55) as the initial

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

• describe the enzyme inhibitor site binding modes [16][17][18]. Thus, in this work, the bisphosphonates 3–6 were synthesized by a two-step method and then evaluated through two in vivo acute inflammation models in BALB/c mice. Furthermore, the acute toxicity was determined for these derivatives, and

• mechanism of action of the bisphosphonates 3–6, we propose that the tested derivatives are acting as MMP inhibitors. In this respect, MMP-8 and MMP-9 isoenzymes are related to inflammatory processes in different tissues [32][33][34][35]. Furthermore, for MMP-8 and MMP-9, enzyme–inhibitor interaction modes

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

• different organisms, enabling researchers to identify and prioritise compounds active against multiple pathogens. For example MMV690102, which was originally developed as an inhibitor of kinetoplastid dihydrofolate reductase [159], is active against three trematode species (F. hepatica, S. haematobium, S

• follow-up study identified two additional pyrazole-5-carboxamide compounds with activity against H. contortus, although not improving on the potency of tolfenpyrad [166]. Tolfenpyrad acts in arthropods as an inhibitor of mitochondrial complex I [167]. It will be interesting if a tolfenpyrad derivative

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

• able to increase the secretion of insulin by the pancreas that modulates blood sugar level when it is high. Sitagliptin was granted FDA approval in October, 2006 [116]. Retagliptin phosphate: Retagliptin phosphate (184) is under investigation as a DPP-4 inhibitor for treating type-2 diabetes. It is an

• synthesis of compound 184 [119][120] (Figure 7). Evogliptin: (R)-2,4,5-Trifluorophenylalanine 38b is required for the synthesis of evogliptin (185, Figure 8), an antidiabetic drug in the dipeptidyl peptidase-4 (DPP-4) inhibitor or "gliptin" class of drugs. The South Korean pharmaceutical company Dong-A ST

• developed evogliptin (185) and it is currently approved for use in South Korea [121][122][123]. LY2497282: Eli Lilly identified LY2497282 (186) as a potent and selective DPP-4 inhibitor, also for the treatment of type II diabetes. The inhibition of GLP-1 degradation by dipeptidyl peptidase IV (DPP-4) has

Efficient synthesis of piperazinyl amides of 18β-glycyrrhetinic acid

• Dong Cai,
• ZhiHua Zhang,
• Yufan Meng,
• KaiLi Zhu,
• LiYi Chen,
• ChangXiang Yu,
• ChangWei Yu,
• ZiYi Fu,
• DianShen Yang and
• YiXia Gong

Beilstein J. Org. Chem. 2020, 16, 798–808, doi:10.3762/bjoc.16.73

• instance, the hydroxy group can be converted into an oxime, acyloxyimino, alkoxyimino, alkoxy and 3-oxo group [9]. As a proteasome inhibitor, compound a suppresses the chymotrypsin-like activity of the proteasome in MT4 cells with an IC50 of 0.22 μM, nearly 100-fold more potent than 18β-glycyrrhetinic acid

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

• [3]. Among these drugs, panobinostat (Farydak, Novartis) an FDA approved drug, has been recognized as a pan-deacetylase inhibitor [9][10]. As a hydroxamic acid pan-HDACi, it is zinc-dependent, capable of binding in a bidentate fashion to the zinc-containing catalytic domain of the HDACs, and

• panobinostat. The reported −log(Kd) values were 8.93, 8.64 and 8.25, respectively, with panobinostat possessing a docking score of 8.47. Considering the effects of structural diversity, TOI3-rev was included in the library and computationally evaluated to determine its potential as an HDAC8 inhibitor. TOI3-rev

• panobinostat against HDAC8 have been shown to be 277 nM [11]. In vivo studies measuring the IC50 values of panobinostat have also been performed, however, since panobinostat is a pan-DAC inhibitor it has been difficult for researchers to specifically correlate its IC50 value for HDAC8 in a physiological system

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

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

• -R indicates C to be a potent inhibitor of P). Compounds: a full range of cheminformatic analysis including 2D or 3D clustering, property prediction and chemical ontology assignments. Proteins: a full range of bioinformatic analysis including gene ontology (GO) assignments, pathway annotation

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

• , compound II4 was safe for weed control in maize fields at a rate of 150 g ai/ha, and was identified as the most potent candidate for a novel HPPD inhibitor herbicide. The compounds described herein may provide useful guidance for the design of new HPPD inhibiting herbicides and their modification

• 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

• of HPPA to HGA is interfered with an HPPD inhibitor [9][10]; consequently, plants become severely damage when exposed to sunlight, ultimately resulting in bleaching symptoms followed by necrosis and death [11][12]. Therefore, HPPD inhibitors play important roles in the herbicide industry. In addition

Synthesis of 3-alkenylindoles through regioselective C–H alkenylation of indoles by a ruthenium nanocatalyst

• Abhijit Paul,
• Debnath Chatterjee,
• Srirupa Banerjee and
• Somnath Yadav

Beilstein J. Org. Chem. 2020, 16, 140–148, doi:10.3762/bjoc.16.16

• the core of proposed anticancer compounds like MIPP and MOMIPP [10], fuligocandin B [2], the TDO inhibitor 680C91 [11], and a HCV NS5B polymerase inhibitor, which has been proposed as a drug against hepatitis C (Figure 1) [12]. The syntheses of 3-alkenylindoles can generally be classified into the

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

• colchicine. It is not the case that colchicine (or any other small-molecule inhibitor) represents an ideal structure that colchicine domain inhibitors (CDIs) should reproduce. Thus, our design focus was to introduce reversible photoresponse to a CDI rather than developing compounds with high similarity to

• is a potent inhibitor of the colchicine binding site (EC50 ≈ 40 nM) with both appropriate solubility and straightforward handling. Self-made low-intensity LED arrays with relatively narrow bandwidth were used for illumination of cells during assays, with a pulsing regime of 75 ms every 15 s to

• photopharmacology. a) The potent tubulin inhibitor colchicine as a lead scaffold led to the development of the HOTub generation of HTI-based antimitotics (e.g., HOTub-31). Changing the lead scaffold to indanocine led to the development of up to ten times more potent HITubs (e.g., HITub-4). b) Straightforward, short

Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion

• Sarah Kölsch,
• Heiko Ihmels,
• Jochen Mattay,
• Norbert Sewald and
• Brian O. Patrick

Beilstein J. Org. Chem. 2020, 16, 111–124, doi:10.3762/bjoc.16.13

• deactivation of a stilbene tyrosine kinase inhibitor by a [2 + 2] photocycloaddition [59]. As the quinolizinium ion has been established as a versatile platform for the development of DNA intercalators [60], we identified styryl-substituted quinolizinium derivatives as a promising basis for the search for

Pigmentosins from Gibellula sp. as antibiofilm agents and a new glycosylated asperfuran from Cordyceps javanica

• Soleiman E. Helaly,
• Wilawan Kuephadungphan,
• Patima Phainuphong,
• Mahmoud A. A. Ibrahim,
• Kanoksri Tasanathai,
• Suchada Mongkolsamrit,
• Janet Jennifer Luangsa-ard,
• Souwalak Phongpaichit,
• Vatcharin Rukachaisirikul and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2968–2981, doi:10.3762/bjoc.15.293

• leave target microbes vulnerable to antibiotics [6]. A complementary approach of using a combination of an antibiotic with a biofilm inhibitor appears to be a promising solution to control biofilm-associated pathogens, as based on the evidence that traditional antibiotics were more effective when used

Palladium-catalyzed synthesis and nucleotide pyrophosphatase inhibition of benzo[4,5]furo[3,2-b]indoles

• Hoang Huy Do,
• Saif Ullah,
• Alexander Villinger,
• Joanna Lecka,
• Jean Sévigny,
• Peter Ehlers,
• Jamshed Iqbal and
• Peter Langer

Beilstein J. Org. Chem. 2019, 15, 2830–2839, doi:10.3762/bjoc.15.276

• nucleotide pyrophosphatase enzyme h-NPP-3. In case of 5e, an inhibitory value IC50 ± SEM = 0.26 ± 0.01 µM was observed which, thus, might be considered as potential inhibitor of h-NPP-3. Compound 5c with an inhibitory value for h-NPP-1 of IC50 ± SEM = 1.29 ± 0.07 µM was more active against NPP1 than against

• . However, the zinc–metal interaction was exhibited by the substituted phenyl moiety on the indole ring. The oxygen atom of the furan ring of dual inhibitor 6e showed a single hydrogen bond with Phe548. Asp423 was found to be involved in two π–cation bindings with the indole ring, whereas π–π stacked, π–π T

• -shaped and π–alkyl related bindings were noticed, connecting Ile235, Phe220, Ala546, Trp322 and Ile419. The fluorine atom was perceived interacting with Ile419. Docking studies of h-ENPP3 inhibitors The binding of ENPP3 was studied for selective inhibitor 5e. A dual affinity was observed for 5h and 6e

An improved, scalable synthesis of Notum inhibitor LP-922056 using 1-chloro-1,2-benziodoxol-3-one as a superior electrophilic chlorinating agent

• Nicky J. Willis,
• Elliott D. Bayle,
• George Papageorgiou,
• David Steadman,
• Benjamin N. Atkinson,
• William Mahy and
• Paul V. Fish

Beilstein J. Org. Chem. 2019, 15, 2790–2797, doi:10.3762/bjoc.15.271

• , Kings Cross, London NW1 1AT, UK 10.3762/bjoc.15.271 Abstract Background: The carboxylesterase Notum has been shown to act as a key negative regulator of the Wnt signalling pathway by mediating the depalmitoleoylation of Wnt proteins. LP-922056 (1) is an orally active inhibitor of Notum. We are

• 1 (or 17) which combines Notum inhibition with CNS penetration would be a valuable chemical probe for investigating the role of Notum in disease models. Keywords: brain penetration; 1-chloro-1,2-benziodoxol-3-one; electrophilic chlorination; LP-922056; Notum inhibitor; Introduction The Wnt

• , Figure 1) is an orally active inhibitor of Notum recently reported by Lexicon Pharmaceuticals [5][6]. Their research with 1 has shown that Notum is a potential drug target for stimulating bone formation and treating osteoporosis [7]. However, although 1 demonstrates low plasma clearance, the structure

Skeletocutins M–Q: biologically active compounds from the fruiting bodies of the basidiomycete Skeletocutis sp. collected in Africa

• Tian Cheng,
• Clara Chepkirui,
• Cony Decock,
• Josphat C. Matasyoh and
• Marc Stadler

Beilstein J. Org. Chem. 2019, 15, 2782–2789, doi:10.3762/bjoc.15.270

• inhibition activity against S. aureus, they showed only weak activity with 20 and 56% inhibition of the biofilm, respectively, at a concentration 256 µg/mL. Tyromycin A (6) was previously reported to be an inhibitor of leucine aminopeptidase in HeLa S3 cells [6]. Accordingly, all compounds 1–5 were tested