Deciphering the mechanism of γ-cyclodextrin’s hydrophobic cavity hydration: an integrated experimental and theoretical study

• Stiliyana Pereva,
• Stefan Dobrev,
• Tsveta Sarafska,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2024, 20, 2635–2643, doi:10.3762/bjoc.20.221

• substituted/modified CDs. Recent studies combining experimental methods with molecular modeling have revealed that the maximum number of water molecules entrapped inside the macrocyclic cavity is 6 for α-CD [13] and 10 for β-CD [14]. Notably, the exact number of the encapsulated water molecules by γ-CD and

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

• compatibility of the GBB reaction with typical KTGS conditions, such as aqueous solvent at near-physiological pH and high dilution, and the achievement of selective ligand amplification. First, molecular modeling studies were carried out to verify that building blocks and intermediates could bind the target

Facile access to pyridinium-based bent aromatic amphiphiles: nonionic surface modification of nanocarbons in water

• Lorenzo Catti,
• Shinji Aoyama and
• Michito Yoshizawa

Beilstein J. Org. Chem. 2024, 20, 32–40, doi:10.3762/bjoc.20.5

• ; Figure S36 in Supporting Information File 1). The formation of spherical particles with narrow size distribution and an average diameter of ≈2 nm was confirmed by DLS and DOSY NMR measurements (Figure 3e and Figure S27 in Supporting Information File 1). Based on molecular modeling, these data suggested

• )m was roughly estimated to be 0.1 mg mL−1. The DLS measurement of (PA-Im)n·(C60)m displayed an average particle diameter of ≈2 nm, which, in combination with molecular modeling, indicated a noncovalent surface functionalization of a single C60 molecule by five PA-Im amphiphiles (Figure 4d,e

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• , and polynucleotide binding affinity has been investigated by UV–vis, fluorescence and CD spectroscopy and molecular modeling. Further, binding of Phen-Py-1 to human dipeptidyl peptidase III enzyme was investigated by fluorescence spectroscopy and microcalorimetric measurements. Results and Discussion

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

• inhibitor:enzyme complexes were analyzed by molecular modeling. Keywords: glycosidase inhibitor; Golgi mannosidase II; iminosugar; inhibition; molecular modeling; Introduction Iminosugars are analogs of monosaccharides in which the endocyclic oxygen atom is replaced with a nitrogen atom [1][2][3][4][5]. These

• inhibitory potential of the investigated imino-ᴅ-lyxitol derivatives. Molecular modeling In order to better understand the results of our inhibition study, the inhibitor:enzyme interactions were analyzed by molecular modeling. Structures of the inhibitors were docked into an X-ray structure of dGMII and

New triazole-substituted triterpene derivatives exhibiting anti-RSV activity: synthesis, biological evaluation, and molecular modeling

• Elenilson F. da Silva,
• Krist Helen Antunes Fernandes,
• Denise Diedrich,
• Jessica Gotardi,
• Marcia Silvana Freire Franco,
• Carlos Henrique Tomich de Paula da Silva,
• Ana Paula Duarte de Souza and
• Simone Cristina Baggio Gnoatto

Beilstein J. Org. Chem. 2022, 18, 1524–1531, doi:10.3762/bjoc.18.161

• molecular modeling with inosine monophosphate dehydrogenase (IMPDH) were performed. Compound 8 was the best performing compound, with an EC50 value of 0.053 μM, a TI of 11160.37 and it inhibited hRSV protein F gene expression by approximately 65%. Molecular docking showed a top-ranked solution located in

• , molecular modeling studies of the interaction of derivative 8 with human IMPDH can provide detailed information regarding the likely mechanism of antiviral action of this molecule. Conclusion In this study, we synthesized new bioisosteric triterpene derivatives of RBV, containing the nitroaryl-1,2,3

First series of N-alkylamino peptoid homooligomers: solution phase synthesis and conformational investigation

• Maxime Pypec,
• Laurent Jouffret,
• Claude Taillefumier and
• Olivier Roy

Beilstein J. Org. Chem. 2022, 18, 845–854, doi:10.3762/bjoc.18.85

• form a unique sheet-like secondary structure, whereas molecular modeling showed that N-aryl peptoid oligomers composed of monomers in the same conformation (as observed in the crystal of dimer 2) might adopt right or left-handed helical conformations that resemble the polyproline type II helix. The χ1

GlycoBioinformatics

• Kiyoko F. Aoki-Kinoshita,
• Frédérique Lisacek,
• Niclas Karlsson,
• Daniel Kolarich and
• Nicolle H. Packer

Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184

• article by Barnett et al. [2] uses molecular dynamics to show that O-linked glycosylation alters peptide conformation, which influences the binding of the peptides to antibodies, despite the fact that glycans are not directly involved in the binding. Another molecular modeling article by Fogarty et al. [3

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

• Kenji Morokuma,
• Shuntaro Tsukamoto,
• Kyosuke Mori,
• Kei Miyako,
• Ryuichi Sakai,
• Raku Irie and
• Masato Oikawa

Beilstein J. Org. Chem. 2021, 17, 540–550, doi:10.3762/bjoc.17.48

• (Figure 10), is therefore, of interest [5], and the synthesis is also underway in our laboratory. Experimental Procedures for all chemical syntheses are described in Supporting Information File 1. Molecular modeling The CONFLEX calculations were performed using BARISTA software (Version 1.2.2.22, Conflex

Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• molecular modeling and the AFM results. The presented crystalline structures are kinetically trapped products since they do not equilibrate upon changing the assembly conditions after they are fully formed. Thus, the addition of THF to preassembled 5%→0% THF crystals up to a 5% THF content did not result in

• different laser powers probed at 755 nm (1 × 10−4 M solution at pH 10): A) 5% THF solution and B) 10% THF solution. Diffusion coefficient and exciton diffusion length. Supporting Information Supporting Information File 92: General information, synthesis, molecular modeling, and further experimental details

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• ). The inhibition by peptide 9 is found to be in a reversible and noncompetitive way. Molecular modeling shows four cationic ammonium groups forming ion pairs and hydrogen bonds with negatively charged residues, such as Glu217, Asp60B, Asp147 and Glu217, respectively and completely block the central pore

• for Direct Fluorescence “Switch‐On” Detection of Nucleic Acid in Cells”, Chem. – Eur. J. © 2017 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim. A) Molecular structure of 6; B) possible binding mode of pyrene termini of 6 to CB[8] according to molecular modeling; C) cartoon representation of ratiometric

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

• acids was monitored by tracking the amide HN and the binding constants were obtained from the resulting binding curves [41]. The binding constants of the amino acids tested cover a ≈ 5-fold range. The differences due to the amino acid side chains were investigated by molecular modeling. Ac-Phe shows the

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

• site of GlfT2, none of these compounds serve as efficient inhibitors of the enzymes involved in the mycobacterial galactan biosynthesis. Keywords: GlfT2; molecular modeling; mycobacterium tuberculosis; synthesis; transition state inhibitors; Introduction Tuberculosis (TB) is one of the most prevalent

• -acetylglucosaminyltransferase I (GnT-I) reaction transition state [11]. Previously, we have designed 2-thiohexofuranoside skeletons bearing a phosphate group in position 1 by molecular modeling as potential transition state inhibitors of human glycosyltransferase I (GnT-I) [12], the bisubstrate enzyme requiring a metal co

• treatment with an excess of 3-chloroperbenzoic acid [16]. Fortunately, the molecular modeling studies did not bring any significant contention about the negative influence of the SO2 group in the target molecule on the standard molecular docking parameters [16]. Based on this fact, a new generation of

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

• based on molecular modeling to understand relationships/interactions between absorbers and a surrounding matrix in the near future. The introduction of functional groups promoting the solubility in water results in absorbers exhibiting an appropriate water solubility, see Table 1 for structures. This

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

• film of the alternating copolymer 6c had a bilayer lamellar structure with 7.3 Å and 22.4 Å distances, respectively (Figure 2b) [13][29][30]. Molecular modeling of the alternating copolymer 6c suggested chain lengths of 11.6 Å and 2.2 Å, respectively. The values of the observed layer distances of

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

• revealed the bioactive binding site positions of potential inhibitors within the targets active site. We modeled the interactions of I12 and II4 (C) with AtHPPD (PDB ID: 1TFZ). The structure of AtHPPD was taken from the PDB data bank. All molecular modeling studies were carried out as previously reported

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

• and showing stability towards harsh acidic conditions. The structural assignment of compound 36 was assessed by detailed 1D and 2D NMR studies, and corroborated with molecular modeling calculations. NOESY-1D experiments carried out with a mixing time of 500 ms allowed to identify the unique rotamer

[1,3]/[1,4]-Sulfur atom migration in β-hydroxyalkylphosphine sulfides

• Katarzyna Włodarczyk,
• Piotr Borowski and
• Marek Stankevič

Beilstein J. Org. Chem. 2020, 16, 88–105, doi:10.3762/bjoc.16.11

• was investigated by molecular modeling (Scheme 9). The first step of the rearrangement involved the protonation of 20, which afforded intermediate I, where the proton inserted between the sulfur and the oxygen atom. This intermediate appeared to be stable and failed to undergo further transformation

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

• regioselectivities were achieved in favor of the 1→3 products due to the equatorial orientation of the OH-3 group. A molecular modeling approach endorsed this general trend of favoring O-3 substitution, although it showed some failures to explain subtler factors governing the difference in regioselectivity between

• some of the acceptors. However, the Galp-(β1→3)-Galp linkage could be regioselectively installed by using some of the acceptors assayed herein. Keywords: Fukui indexes; galactopyranosyl acceptors; galactose donors; molecular modeling; regioselectivity; Introduction Given the importance of

• molecular modeling approach. Results and Discussion For this study, ᴅ-Galp derivatives with both their OH-2 and OH-6 group blocked were required. The regioselective functionalization of carbohydrates is usually a difficult task due to the similar reactivity of secondary hydroxy groups [13]. We synthesized

Sugar-derived oxazolone pseudotetrapeptide as γ-turn inducer and anion-selective transporter

• Sachin S. Burade,
• Sushil V. Pawar,
• Tanmoy Saha,
• Navanath Kumbhar,
• Amol S. Kotmale,
• Manzoor Ahmad,
• Pinaki Talukdar and
• Dilip D. Dhavale

Beilstein J. Org. Chem. 2019, 15, 2419–2427, doi:10.3762/bjoc.15.234

• the oxazolone pseudo-peptide showed intramolecular C=O···HN(II) hydrogen bonding in a seven-membered ring leading to a γ-turn conformation. This fact was supported by a solution-state NMR and molecular modeling studies. The oxazolone pseudotetrapeptide was found to be a better Cl−-selective

• thus supported the presence of γ-turn helical type conformation of 2a. Molecular modeling studies In order to corroborate our results, obtained from the NMR studies, the molecular modeling study was performed using Spartan’14 software [29][30]. The initial geometry of 2a, generated from the NOESY study

• . The molecular modeling study of N-acetylated compound 2b also indicated the presence of a seven-membered hydrogen bonding between NH(II) and –C=O [bond distance (d) = 2.74 Å and bond angle (NH···O) = 112.98°] suggesting the presence of a γ-turn conformation (Figure 5B). Ion transport activity The

Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• details Different molecular modeling methods (quantum mechanics (QM), molecular dynamics (MD), docking and quantitative structure activity relationships (QSARs)) can be applied in studying the structure, dynamics, and energetics of the host CD systems. However, the results from different modeling (or

Synthesis, biophysical properties, and RNase H activity of 6’-difluoro[4.3.0]bicyclo-DNA

• Sibylle Frei,
• Adam K. Katolik and
• Christian J. Leumann

Beilstein J. Org. Chem. 2019, 15, 79–88, doi:10.3762/bjoc.15.9

• [43][44] followed by phosphitylation at the 3’-oxygen afforded the phosphoramidite 9. X-ray structure and molecular modeling of the 6’-diF-bc4,3 nucleoside To verify the relative configuration of nucleoside 6, crystals of this compound were subjected to X-ray diffraction analysis. The asymmetric unit

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• Sibylle Frei Andrei Istrate Christian J. Leumann Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland 10.3762/bjoc.14.288 Abstract Here we report on the synthesis, biophysical properties and molecular modeling of oligonucleotides containing

• structure, giving evidence of mixed A/B-type helices. Molecular modeling To gain more information on the structural features of the 6’F-bc4,3 modification, we performed molecular dynamics simulations of the modified duplexes. We first calculated the potential energy profile versus pseudorotation phase angle

Synthesis and photophysical studies of a multivalent photoreactive Ru^II-calix[4]arene complex bearing RGD-containing cyclopentapeptides

• Sofia Kajouj,
• Lionel Marcelis,
• Alice Mattiuzzi,
• Adrien Grassin,
• Damien Dufour,
• Pierre Van Antwerpen,
• Didier Boturyn,
• Eric Defrancq,
• Mathieu Surin,
• Julien De Winter,
• Pascal Gerbaux,
• Ivan Jabin and
• Cécile Moucheron

Beilstein J. Org. Chem. 2018, 14, 1758–1768, doi:10.3762/bjoc.14.150

• attributed to [9 + H]3+, [9 + 2H]4+ and [9 + 3H]5+ by comparison between the experimental and theoretical isotope distributions (see Supporting Information File 1). Molecular modeling simulations were carried out to provide insights into the size and morphology of conjugate 9. An optimized geometry is

• systems that could potentially target and enter cancer cells. The selective tethering of a photoreactive Ru-TAP complex on the small rim of a calix[4]arene and the introduction of four c-[RGDfK] moieties on its large rim were efficiently achieved. In good agreement with molecular modeling simulations, it