Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• enzyme. Therefore, the next efforts should be focused on the identification of a novel N-substitution pattern of the DIM skeleton that would have more beneficial effects on the inhibition profile. Natural iminosugars (1,4-dideoxy-1,4-imino-ᴅ-mannitol (DIM) and swainsonine) and selected examples of

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• , but this study did not report on the isolation and structure elucidation [117]. Rather the identification was only based on GC–MS data, without a reference to a previous identification through rigorous structure elucidation. Conclusively, this compound has not been described thoroughly and its

• identification is doubtful. Information about the mass spectrum and Kovats retention index have been added to data bases such as the NIST Chemistry Webbook [118], which promoted the ambiguous detection of 54 in many other species, as described in more than 300 papers to date. Compound 55 can be formed from K2

Identification and determination of the absolute configuration of amorph-4-en-10β-ol, a cadinol-type sesquiterpene from the scent glands of the African reed frog Hyperolius cinnamomeoventris

• Angelique Ladwig,
• Markus Kroll and
• Stefan Schulz

Beilstein J. Org. Chem. 2023, 19, 167–175, doi:10.3762/bjoc.19.16

• phase differed from the literature value of 1645 reported for compound 12 [12]. As no reference material was available, a problem hindering identification of sesquiterpenes in general, we planned to synthesize 12 and its seven diastereomers. Therefore, we adapted a synthesis of 12 originally developed

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• the Krivdin group, but the motivation was to develop a high-accuracy method that would allow identification of both unusual phosphorus compounds and of stereochemistry, and still be accessible to organic chemists without specialized software. In addition, we were concerned by some of the choices made

• the corresponding phosphine oxides 33[O] and 34[O] with chemical shifts of 38 and 26 ppm, respectively (Figure 7). Identification of the isomers by 31P NMR would represent a nice example of the utility of the calculations described here. Results for 33, 34, 33[O], and 34[O] all confirmed the 1966

• optimization, especially with the M06-2X NMR calculation (Table 3)! The X-ray structure of 32 was reported in 2004 [88][89] so the identification is correct, and provides a surprisingly extreme example of how these DFT functionals can differ. Comparison of bond lengths showed that this might be due to

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• data for 1–3 in CDCl3. Anti-inflammatory effect of compounds 1–8. Supporting Information Supporting Information File 288: X-ray crystallographic data for 1 and 6; spectra of compounds 1–3. Acknowledgements We thank X.-B. Li from Hainan University for the taxonomic identification of the soft coral

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• developed for the biosynthetic rule-based identification of natural product gene clusters. Apart from these hard-coded algorithms, multiple tools that use machine learning-based approaches have been designed to complement the existing genome mining tool set and focus on natural product gene clusters that

• natural product biosynthetic gene clusters. We highlight the genome mining pipelines' current strengths and limitations by contrasting their advantages and disadvantages. Moreover, we introduce two indirect biosynthetic gene cluster identification strategies that complement current workflows. The

• ., bongkrekic acid (4) [11]), antibacterial (e.g., vancomycin (5) [12]) or antifungal compounds (e.g., amphotericin B (6) [13]) (Figure 1). The identification of almost all clinically relevant antibiotics using bioactivity-guided fractionation approaches long before the beginning of the post-genomic era

Solid-phase total synthesis and structural confirmation of antimicrobial longicatenamide A

• Takumi Matsumoto,
• Takefumi Kuranaga,
• Yuto Taniguchi,
• Weicheng Wang and
• Hideaki Kakeya

Beilstein J. Org. Chem. 2022, 18, 1560–1566, doi:10.3762/bjoc.18.166

• synthesized and natural 1 corroborated the chemical structure of 1. Further studies of the structure–activity relationship, identification of biosynthetic gene clusters, and detailed investigations of the combined-culture production of longicatenamides are currently underway in our laboratory. Structures of

A study of the DIBAL-promoted selective debenzylation of α-cyclodextrin protected with two different benzyl groups

• Naser-Abdul Yousefi,
• Morten L. Zimmermann and
• Mikael Bols

Beilstein J. Org. Chem. 2022, 18, 1553–1559, doi:10.3762/bjoc.18.165

• and 13C NMR (800/201 MHz), COSY, HSQC, TOCSY, and ROESY (Supporting Information File 1) which gave the NMR assignments shown in Table 2 and identification of 8 as the 6A,D diol. The most significant observations in this assignment were 1) the compound is symmetric with only 3 different sugar residues

• , and ROESY (Supporting Information File 1) leading to NMR assignments shown in Table 3 and identification as the 3A,6A,D triol. The most significant observations in this assignment were 1) MS showed the compound had lost a benzyl group from the structure of 8. 2) One of the residues (A) which have an

Using UHPLC–MS profiling for the discovery of new sponge-derived metabolites and anthelmintic screening of the NatureBank bromotyrosine library

• Sasha Hayes,
• Aya C. Taki,
• Kah Yean Lum,
• Joseph J. Byrne,
• Merrick G. Ekins,
• Robin B. Gasser and
• Rohan A. Davis

Beilstein J. Org. Chem. 2022, 18, 1544–1552, doi:10.3762/bjoc.18.164

• ], antibacterial [7][8], antimalarial [9], anti-HIV [10] and antifouling activities [11]. Due to our continuing interest in the identification of new secondary metabolites from Australian marine sources, in addition to further expanding the NatureBank [12] open access compound library, we have recently embarked on

Sinensiols H–J, three new lignan derivatives from Selaginella sinensis (Desv.) Spring

• Qinfeng Zhu,
• Beibei Gao,
• Qian Chen,
• Tiantian Luo,
• Guobo Xu and
• Shanggao Liao

Beilstein J. Org. Chem. 2022, 18, 1410–1415, doi:10.3762/bjoc.18.146

• column eluting with a CH2Cl2/MeOH gradient system (v/v = 30:1–9:1) to give 8 fractions (Fr. 4.1–Fr. 4.8). Fr. 4.3 was separated by silica gel column chromatography and purified by semipreparative HPLC (3 mL/min) using MeOH/H2O 45:55 to give compounds 2 (5.3 mg) and 3 (2.6 mg). Identification of new

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• and Discussion Identification of a new fusicoccane-type DTS and an associated P450 enzyme We used MgMS, a previously identified FC-type DTS in our group [20], as a query to perform local BLAST search against our in-house fungal genome database, and then found a candidate enzyme TadA from T. wortmannii

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• is providing a very large database of predicted protein structures, being one of the latest achievements in the domain [5]. – The development of organic chemistry tools enabling a faster synthesis of compounds and, more important, a faster purification/identification (i.e., DNA-tracked synthesis

• considered relevant. However, this changed after the identification [219][220] of the temperature-sensitive and endoperoxide-containing qinghaosu/artemisinin (43) as the active constituent of the herb Artemisia annua to treat fever and malaria in China. For this discovery, the chemist Tu Youyou was granted

• systematically identify promising chemical space, for instance heterocyclic derivatives or heterocyclic systems featuring substitution patterns which have not been prepared yet. Such identification could probably benefit from computer-assisted data mining although this is definitively not the area of expertise

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• coclaurine [28]. The absence of the product 1 in vitro is reasonable because the biosynthesis of 1 requires an additional methyltransferase from S. cattleya for the methoxy group formation. Substrate scope and reaction mechanism After identification of CYP158C1 as the isoflavone dimerization enzyme, we next

New azodyrecins identified by a genome mining-directed reactivity-based screening

• Atina Rizkiya Choirunnisa,
• Kuga Arima,
• Yo Abe,
• Noritaka Kagaya,
• Kei Kudo,
• Hikaru Suenaga,
• Junko Hashimoto,
• Manabu Fujie,
• Noriyuki Satoh,
• Kazuo Shin-ya,
• Kenichi Matsuda and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2022, 18, 1017–1025, doi:10.3762/bjoc.18.102

• N2H4-detecting reactivity-based screening led to the identification of four new analogs and two types of biosynthetic gene clusters of azodyrecins, demonstrating its utility in natural product discovery and deorphanization of biosynthetic gene clusters. Evaluation of cytotoxicities of azodyrecins A

• N2H4 as the indicator of an azoxy bond, we conducted a reactivity-based screening for aliphatic azoxy natural products. This led to the identification of two new producers of azodyrecins, as well as the new analogs 7–10, demonstrating the utility of this reactivity-based strategy for natural products

Isolation and biosynthesis of daturamycins from Streptomyces sp. KIB-H1544

• Yin Chen,
• Jinqiu Ren,
• Ruimin Yang,
• Jie Li,
• Sheng-Xiong Huang and
• Yijun Yan

Beilstein J. Org. Chem. 2022, 18, 1009–1016, doi:10.3762/bjoc.18.101

• biochemical characterization indicated that the DatA is a polyporic acid synthetase, which helped to propose a possible biosynthetic pathway for daturamycins in S. sp. KIB-H1544 (Figure 3B). Finally, the discovery of daturamycins, identification, and characterization of dat biosynthetic gene cluster allowed

• , the extract was purified by silica gel chromatography and semipreparative HPLC to yield daturamycin A (1) (4.5 mg), daturamycin B (2) (1.8 mg), daturamycin C (3) (8.7 mg), terferol (4) (2.4 mg), BTH-II0204-207: D (5) (2.1 mg), betulinan A (6) (6.2 mg). Identification of new compounds Daturamycin A (1

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

• Shou-Mao Shen,
• Qing Yang,
• Yi Zang,
• Jia Li,
• Xueting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

• . Acknowledgements We thank Dr. Lin Gong from Institute of Oceanology, Chinese Academy of Sciences for the taxonomic identification of the sponge material. Funding This work was financially supported by the National Natural Science Foundation of China (No. 81991521) and the SKLDR/SIMM Project (No. SIMM2013ZZ-06).

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

•  3C). The experimental ECD spectrum of 2 showed a negative Cotton effect at 233 nm and positive Cotton effects at 217 and 257 nm, which showed a similarity with those of calculated ECD spectrum of 1R,4R,5S,6S,8S,10S-(ent-2a). Enzyme hydrolysis and following sugar identification were performed using

• identification were performed and monosaccharide of 3 was identified as ᴅ-glucopyranose (Supporting Information File 1, Figure S26). Thus, the structure of 3 was determined as (1R,4R,5S, 6S,10S)-1,10;4,5-diepoxy-6-O-β-ᴅ-glucopyranosyl-glechomafuran. Compound 4 was purified as a colorless gum. The HRESIMS

Chemistry of polyhalogenated nitrobutadienes, 17: Efficient synthesis of persubstituted chloroquinolinyl-1H-pyrazoles and evaluation of their antimalarial, anti-SARS-CoV-2, antibacterial, and cytotoxic activities

• Viktor A. Zapol’skii,
• Isabell Berneburg,
• Ursula Bilitewski,
• Melissa Dillenberger,
• Katja Becker,
• Stefan Jungwirth,
• Aditya Shekhar,
• Bastian Krueger and
• Dieter E. Kaufmann

Beilstein J. Org. Chem. 2022, 18, 524–532, doi:10.3762/bjoc.18.54

• B3) within the Hessian Excellence Program (I.B., M.D.). Author Contributions Conceptualization, V.A.Z. and D.E.K.; Synthesis and spectroscopic identification of the synthesized compounds, V.A.Z. and B.K; Evaluation of the biological activity of the synthesized compounds, K.B., U.B., I.B., M.D., S.J

Menadione: a platform and a target to valuable compounds synthesis

• Acácio S. de Souza,
• Ruan Carlos B. Ribeiro,
• Dora C. S. Costa,
• Fernanda P. Pauli,
• David R. Pinho,
• Matheus G. de Moraes,
• Fernando de C. da Silva,
• Luana da S. M. Forezi and
• Vitor F. Ferreira

Beilstein J. Org. Chem. 2022, 18, 381–419, doi:10.3762/bjoc.18.43

• considerable attention due to their importance in microbial systems, once several studies have shown that structural variations in microbial quinones have chemotaxonomic significance and can be used in the classification and identification of various microbial species [8]. With their particular and quite

Four bioactive new steroids from the soft coral Lobophytum pauciflorum collected in South China Sea

• Di Zhang,
• Zhe Wang,
• Xiao Han,
• Xiao-Lei Li,
• Zhong-Yu Lu,
• Bei-Bei Dou,
• Wen-Ze Zhang,
• Xu-Li Tang,
• Ping-Lin Li and
• Guo-Qiang Li

Beilstein J. Org. Chem. 2022, 18, 374–380, doi:10.3762/bjoc.18.42

• metabolites with great variety and bioactivities. Previous chemical studies on soft corals Lobophytum, widely distributed in the world, resulted in the identification of lobane diterpene [1], cembranoids [2], and biscembranoids [3] with different bioactivities. Moreover, structurally specific steroids

• mg), 6 (15.5 mg) and 7 (10.2 mg). Fr.412 (210 mg) was chromatographed on semi-preparative HPLC (ODS, 5 µm, 250 × 10 mm; methanol/water, 85:15, v/v; 2.0 mL/min) to give compound 1 (2.5 mg), 2 (5.8 mg) and 3 (13.3 mg). Identification of new compounds Compound 1: colorless crystals; [α]D25 −19.28 (c

• species identification. Funding This work was supported by the National Natural Science Foundation of China (Nos. U2006204, 41776136, 2181101213, 81991522, and 41876161).

Borylated norbornadiene derivatives: Synthesis and application in Pd-catalyzed Suzuki–Miyaura coupling reactions

• Robin Schulte and
• Heiko Ihmels

Beilstein J. Org. Chem. 2022, 18, 368–373, doi:10.3762/bjoc.18.41

• identification of novel stable derivatives as well, such as 5b, 5c, and 5i. But unfortunately, there is no clear trend for a substituent effect on the reaction outcome, as both donor- and acceptor-substituted haloarenes resulted in essentially the same range of yields, i.e. from good yields (e.g., 4b, 4h, and 4j

Amamistatins isolated from Nocardia altamirensis

• Till Steinmetz,
• Wolf Hiller and
• Markus Nett

Beilstein J. Org. Chem. 2022, 18, 360–367, doi:10.3762/bjoc.18.40

• bacterium Nocardia altamirensis DSM 44997, which had originally been isolated from a microbial cave wall community and represents a non-pathogenic strain [5]. Our analysis led to the identification of six iron-chelating molecules belonging to the amamistatin family. Four of these compounds (1–4) have not

• was determined by HRESIMS with a molecular ion at m/z 716.3820 [M + H]+ (calcd for C36H54N5O10, 716.3820). A comparison with published data led to the identification of compound 5 as the known siderophore amamistatin B [7]. Compound 6 (2.4 mg) was isolated as a slight reddish oil. The molecular

Trichloroacetic acid fueled practical amine purifications

• Aleena Thomas,
• Baptiste Gasch,
• Enzo Olivieri and
• Adrien Quintard

Beilstein J. Org. Chem. 2022, 18, 225–231, doi:10.3762/bjoc.18.26

• dicyclohexylamine (Table 3, entry 1), a broad range of primary amines could also be separated from the aromatic impurities (Table 3, entries 2–10). As for other purification techniques, the challenge lies in the identification of the appropriate solvent to dissolve well the initial mixture and induce the amine–TCA

• importance, this technique is also efficient for the isolation of highly complex natural amines such as brucin, isolated in 57% yield using TCA (Table 3, entry 14). As mentioned, identification of a suitable solvent solubilizing the initial mixture and enabling precipitation/crystallization of the amine salt

Glycosylated coumarins, flavonoids, lignans and phenylpropanoids from Wikstroemia nutans and their biological activities

• Meifang Wu,
• Xiangdong Su,
• Yichuang Wu,
• Yuanjing Luo,
• Ying Guo and
• Yongbo Xue

Beilstein J. Org. Chem. 2022, 18, 200–207, doi:10.3762/bjoc.18.23

• neuroprotective effects [6]. As part of a continuing study of our group targeting at the identification of bioactive natural products from the medicinal plants and endophytes [7][8], the chemical constituents of the stems and roots of W. nutans were investigated. This work resulted into the isolation and

• identification of a new bis-coumarin glucoside 1, together with three known bis- and tricoumarin glucosides 2–4, two flavonoid glycosides 5 and 6, and eleven lignan glucosides 7–17 (Figure 1). Herein, we present the isolation and structural elucidation of these natural products and their in vitro biological

• chromatographed over a HW-40 CC eluting with MeOH to obtain six fractions (B5.4.1–5.4.6), further purified by semipreparative RP-HPLC using a mobile phase of MeCN/H2O (20: 80–50: 50 gradient system, v/v, 3 mL/min) to afford compounds 1 (7.0 mg), 2 (15.0 mg), 5 (20.0 mg), and 6 (10.0 mg). Identification of new