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

• Km or Ki values of the structures similar to the studied compounds were not available and therefore we were not able to create a more precise linear regression model for the binding affinity prediction. For this reason, we could use only a coarse correction for the calculated Ki values and the

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• , developing property prediction algorithms and now for ML and AI applications. In this case, external conditions apply that lead to a different ontology than the two others. We discuss some features of these languages in the following and relate them to existing concepts. The title “Models of necessity

• used far more often as descriptors in this context, although the adequacy of these descriptors for reaction prediction has been questioned [40]. The role of models in describing molecules and reactions for AI and ML Only thirty years’ ago, before the advent of everyday computer graphics programs and

• since chemists reached an understanding of chemical structures, there is still no all-encompassing theory to enable accurate prediction of structure–activity or structure–function relationships. Chemistry remains a confusing science in which the often overlapping concepts of models, approximations

In silico rationalisation of selectivity and reactivity in Pd-catalysed C–H activation reactions

• Liwei Cao,
• Mikhail Kabeshov,
• Steven V. Ley and
• Alexei A. Lapkin

Beilstein J. Org. Chem. 2020, 16, 1465–1475, doi:10.3762/bjoc.16.122

• automated reaction planning, as well as a starting point for microkinetic modelling. Keywords: C–H activation; density functional theory; reaction prediction; Introduction Periodically, our knowledge of chemistry is enriched with new transformations that provide significant breakthroughs by enabling new

• ) and artificial intelligence (AI) tools [7][8][9]. Especially the methods of ML/AI for prediction of reaction outcomes are attracting a lot of attention. Prediction accuracies in the order of 70–80% for the reaction outcomes [9], and around 60–70% for reaction conditions [10], were recently

• for in silico prediction of reaction outcomes. This approach was tested on the for green chemistry important class of C–H activation reactions. Whilst this study does not completely solve the problem of developing a robust chemical reaction, it offers an approach that is complementary to efforts of

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

• molecular modification of the derivatives 1 and 2 through the bioisosteric replacement [20] of the amide functional group by an aliphatic or aromatic ester. The potential antiinflammatory activity of the new bisphosphonates was predicted using the Prediction of Activity Spectra for Substances (PASSOnline

• ) database, which compares the molecular structure of test compounds vs a large training set of experimental bioactive or inactive compounds [21]. The results of the prediction are summarized as probability of activity (Pa) and probability of inactivity (Pi) values, both ranging from 0 to 1 (Figure 2), where

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

• resulting from the 60-AR_RNA cleavage. Prediction of the RNA secondary structure with the folding energy before and after cleavage was performed by MFold open source [21]. The SDFS functional activity. A–C) Emission spectra of the assembled SDFS (green line), T1–T5 chains mix without annealing (green dotted

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

• chemical shift prediction [22][23][24]. 1H and 13C NMR chemical shifts were obtained for two possible diastereomers, (2R,2'S,2''S)-isomer (1a) and (2S,2'S,2''S)-isomer (1b), by calculation at the mPW1PW91/6-31G+(d,p)-PCM (DMSO) level of theory (Tables S1 and S2 in Supporting Information File 2). The

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

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• studies seem to allow the prediction of the activity of derivatives able to pass intersystem crossing to their triplet energy state and thus create radicals able to damage DNA. With this study, it is shown that oxime carbamate derivatives have the potential to act as novel effective photobase generating

• the radical τ = 1ps. This is in complete agreement with the prediction made by McBurney and Walton [51] for the decarboxylation of N-arylcarbamoyloxyl radicals where they were expected to decarboxylate with great rapidity having almost no finite lives. Excitation of 12 to the singlet excited state (S1

Formal preparation of regioregular and alternating thiophene–thiophene copolymers bearing different substituents

• Atsunori Mori,
• Keisuke Fujita,
• Chihiro Kubota,
• Toyoko Suzuki,
• Kentaro Okano,
• Takuya Matsumoto,
• Takashi Nishino and
• Masaki Horie

Beilstein J. Org. Chem. 2020, 16, 317–324, doi:10.3762/bjoc.16.31

• , 1134, 1052, 840, 801, 773, 754, 720, 700 cm−1. Solubility tests of alternating copolymer 6 (1 mg of material dissolved in 1 mL of the solvent). XRD measurement and prediction of the bilayer lamellar structure of polymer 6c. a) XRD analysis. b) Suggested bilayer lamellar structure. c) Side chain length

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

• PCA score prediction. SMILES codes for all compounds were retrieved using ChemBioDraw Ultra 12.0 and submitted to ChemGPS-NP for achieving the corresponding PC scores (see Supporting Informations). The PCA data were then used for the construction of PC1 vs PC2. PMI analysis. Principal moments of

Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds

• Vuyisa Mzozoyana,
• Fanie R. van Heerden and
• Craig Grimmer

Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22

• not necessarily be observed. This is consistent with the idea of an average angle in solution that places the fluorine atom closer to H5 than H3, since F–H5 coupling is obvious in the experimental NMR spectrum (Figure 1), while F–H3 coupling is not. A similar prediction is made for coupling between F

Regioselectivity of glycosylation reactions of galactose acceptors: an experimental and theoretical study

• Enrique A. Del Vigo,
• Carlos A. Stortz and
• Carla Marino

Beilstein J. Org. Chem. 2019, 15, 2982–2989, doi:10.3762/bjoc.15.294

• coefficients (Table 2). Nevertheless, the change in selectivity predicted for the benzylated diol analogs of 1α/1β did not match the experimental trend. Similar results were observed with the M06-2X functional (Table 2). The calculations gave a good prediction of the higher OH-3 group’s reactivity, but an

• accurate prediction of the trends in selectivity could not be achieved. We have tried to explain the reduced regioselectivity of the β-anomers through hydrogen bonding interactions of the OH-3 and OH-4 groups of the model acceptors. Doutheau and co-workers proposed that such a reduced regioselectivity

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

• -derived terpene-modifying enzymes. In addition, the fact that several CYPs have been shown to have relaxed substrate specificity, act on several intermediates, or catalyze multiple reactions, further complicates the in silico prediction. (Bio)synthetic production of complex terpenoids Heterologous

• /surrogate redox partners or fusing CYPs with redox partners [80][136][141][150][151]. One common observation is that CYP activity is not able to match the high flux of isoprenoids, leaving a significant portion of terpenes unmodified. Solutions to this problem, such as in silico redox partner prediction

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

• in protein data bank (PDB). For the prediction of the 3D homology prototype, the reported structure of mouse ENPP1 with PDB ID 4B56, was used as standard pattern [43]. Molecular Operating Environment (2014. 0901) was used for this purpose. The modeled crystal structures manifested 80% for ENPP1 and

Experimental and computational electrochemistry of quinazolinespirohexadienone molecular switches – differential electrochromic vs photochromic behavior

• Eric W. Webb,
• Jonathan P. Moerdyk,
• Kyndra B. Sluiter,
• Benjamin J. Pollock,
• Amy L. Speelman,
• Eugene J. Lynch,
• William F. Polik and
• Jason G. Gillmore

Beilstein J. Org. Chem. 2019, 15, 2473–2485, doi:10.3762/bjoc.15.240

• ] were in very good agreement with those determined experimentally (Table 1). The mean absolute deviation between computational prediction and experimental measurement of Eored for all SW and LW structures in Table 1 is just 21 mV (27 mV root mean squared deviation), not far from the 14 mV mean standard

• that the N–C bond which breaks upon forming the LW product would possess a smaller bond order. The BO calculations for intermediate states T0 and D0 indeed support this prediction. Table 2 summarizes the results of BO calculations for both bonds in these states. Since geometry plays a critical role in

Genome mining in Trichoderma viride J1-030: discovery and identification of novel sesquiterpene synthase and its products

• Xiang Sun,
• You-Sheng Cai,
• Yujie Yuan,
• Guangkai Bian,
• Ziling Ye,
• Zixin Deng and
• Tiangang Liu

Beilstein J. Org. Chem. 2019, 15, 2052–2058, doi:10.3762/bjoc.15.202

• the combination of genome mining and heterologous expression of predicted terpene synthases for detecting unknown terpenoids from rarely studied fungi. Results and Discussion Prediction and analysis of terpene synthase genes in T. viride J1-030 Through genome sequencing of T. viride J1-030 and

• prediction of the potential terpene synthases in J1-030 genome, gene Tvi09626 was selected and the following bioinformatics analysis of the function of this unidentified terpene synthase was performed. A protein blast search against the NCBI database was performed with Tvi09626, revealing sequence identities

Synthesis and anion binding properties of phthalimide-containing corona[6]arenes

• Meng-Di Gu,
• Yao Lu and
• Mei-Xiang Wang

Beilstein J. Org. Chem. 2019, 15, 1976–1983, doi:10.3762/bjoc.15.193

• . Upon complexation with a halide, the planar aromatic ring adopted a heavily pinched boat conformation, a result consistent with theoretical prediction [49]. We also examined the host–guest interaction in solution phase employing NMR and UV–vis spectroscopy and fluorescence technology. Unfortunately

Host–guest interactions between p-sulfonatocalix[4]arene and p-sulfonatothiacalix[4]arene and group IA, IIA and f-block metal cations: a DFT/SMD study

• Valya K. Nikolova,
• Cristina V. Kirkova,
• Silvia E. Angelova and
• Todor M. Dudev

Beilstein J. Org. Chem. 2019, 15, 1321–1330, doi:10.3762/bjoc.15.131

• by the negative Gibbs free energy values (ΔG1 and ΔG78). The combination of implicit/explicit solvent treatment seems useful in the modeling of the p-sulfonatocalix[4]arene (and thiacalix[4]arene) complexes with metal cations and in the prediction of the thermodynamic parameters of the complex

Genomics-inspired discovery of massiliachelin, an agrochelin epimer from Massilia sp. NR 4-1

• Jan Diettrich,
• Hirokazu Kage and
• Markus Nett

Beilstein J. Org. Chem. 2019, 15, 1298–1303, doi:10.3762/bjoc.15.128

• [23]. An analysis of the analogous enzymes in micacocidin [13], yersiniabactin [16], and enantio-pyochelin [24] biosynthesis confirmed that the presence or absence of this feature allows a reliable prediction of the stereochemistry in this position (Table S1, Supporting Information File 1). In every

• single case, the domain-based configurational prediction matched the experimental assignment [24][25][26][27][28]. By applying this method to the MicC homolog from Massilia sp. NR 4-1, the presence of a D-thiazoline ring in 1 can be deduced. Moreover, the thiazolidine ring in 1 must have the

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• , albeit more indirect, comes from an inhibition study using omeprazole, which was predicted to possibly interact with ThDP-dependent enzymes. The prediction was based on the similarity of omeprazole to the tricyclic form of thiamin. This was confirmed experimentally when omeprazole was subsequently shown

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• mannose-specific C-type lectins from Caenorhabditis elegans, Mus musculus, and Homo sapiens (see Figure 5 for partial secondary structure prediction and alignment with the human C-type mannose receptor 2) [77][78], and is predicted to be localized to the outer membrane [93]. While Rv2075c orthologues have

• have been found in glycosyltransferases as well as in bacterial hydrolases [95]. The Mtb gene product of Rv1419 shows 41% amino acid sequence similarity to R-type lectins and encodes the Mtb protein sMTL-13 (see Figure 5 for secondary structure prediction and alignment with the ricin B-like lectin from

Ring-opening metathesis of some strained bicyclic systems; stereocontrolled access to diolefinated saturated heterocycles with multiple stereogenic centers

• Zsanett Benke,
• Melinda Nonn,
• Márton Kardos,
• Santos Fustero and
• Loránd Kiss

Beilstein J. Org. Chem. 2018, 14, 2698–2707, doi:10.3762/bjoc.14.247

• different results in view of the used Ru-based catalyst, which allowed us to conclude that all these transformations are highly substrate and catalyst dependent, the nature of the structure of the cyclic starting material determining the outcome of the transformations. It is well known that the prediction

Learning from B₁₂ enzymes: biomimetic and bioinspired catalysts for eco-friendly organic synthesis

• Keishiro Tahara,
• Ling Pan,
• Toshikazu Ono and
• Yoshio Hisaeda

Beilstein J. Org. Chem. 2018, 14, 2553–2567, doi:10.3762/bjoc.14.232

• liquid layer could be recycled for further reactions. More interestingly, the catalytic ability of 1 increased nearly four times the reaction using DMF as solvent. This was consistent with the Hughes–Ingold prediction of solvent polarity effects on reaction rates [111]. We also developed a visible-light

Determining the predominant tautomeric structure of iodine-based group-transfer reagents by ¹⁷O NMR spectroscopy

• Nico Santschi,
• Cody Ross Pitts,
• Benson J. Jelier and
• René Verel

Beilstein J. Org. Chem. 2018, 14, 2289–2294, doi:10.3762/bjoc.14.203

• estimate of ±10 ppm. While 5a/b indeed has been shown to exist as the thioperoxide 5b (vide infra), a crystallographic study on 6a/b is required to corroborate our prediction as 6a. To further gauge the utility of this approach, the activation of Togni reagent 4a was studied, in particular its protonation