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

• molecules also presented this type of interactions between an ethyl fragment of the ligand with Leu160, and less with His207 and Val194. Weak hydrophobic interactions were also observed from Tyr219 and the aromatic ring of 6 as well as π–π interactions to His197. The molecules were not adequately occupying

• from the aromatic ring of the ligands 5 and 6 with the Phe110 residue were displayed (Figure 5c and 5d). Furthermore, CH–π interactions from the tert-butyl group with Phe110 were also seen, with a 3.12 Å distance (Figure 5b). All molecules had hydrophobic interactions from an ethyl group of the ligands

• = zinc complexation; highlighted in blue = most relevant residues; dashed pink lines = π–π interactions; grey = hydrophobic interactions. 2D schematic representations of the MMP-9 catalytic site, with 3–6 and the most relevant interactions. Red = hydrogen bonds; dotted bonds = zinc complexation

Fluorinated maleimide-substituted porphyrins and chlorins: synthesis and characterization

• Valentina A. Ol’shevskaya,
• Elena G. Kononova and
• Andrei V. Zaitsev

Beilstein J. Org. Chem. 2019, 15, 2704–2709, doi:10.3762/bjoc.15.263

• on 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin (1) as the starting compound. The presence of fluorine atoms on the four phenyl rings at the meso-positions of the porphyrin structure can make a strong influence on the hydrophobic interactions and lipophilicity, metabolic stability, thus modulating

Synthetic terpenoids in the world of fragrances: Iso E Super^® is the showcase

• Alexey Stepanyuk and
• Andreas Kirschning

Beilstein J. Org. Chem. 2019, 15, 2590–2602, doi:10.3762/bjoc.15.252

• challenges to be solved. Hydrophilic and hydrophobic interactions with the unpolar lipid layer make the tendency to yield suitable crystals even more difficult. Nevertheless, Palczewski and co-workers were able to crystallise the first GPCR (G-protein-coupled receptor) in 2000 confirming the previously

Archangelolide: A sesquiterpene lactone with immunobiological potential from Laserpitium archangelica

• Silvie Rimpelová,
• Michal Jurášek,
• Lucie Peterková,
• Jiří Bejček,
• Vojtěch Spiwok,
• Miloš Majdl,
• Michal Jirásko,
• Miloš Buděšínský,
• Juraj Harmatha,
• Eva Kmoníčková,
• Pavel Drašar and
• Tomáš Ruml

Beilstein J. Org. Chem. 2019, 15, 1933–1944, doi:10.3762/bjoc.15.189

• Information File 1, Table S4). Nevertheless, the complex of SERCA with thapsigargin is preferentially stabilized by hydrophobic interactions, [21] and all three mentioned SLs are strongly hydrophobic molecules. We therefore assumed that compounds 1 and 2, which can form even fewer hydrogen bonds than

• ). The first round of simulations (1–10 ns) of compound 1 docking into SERCA cavity with compound 1 constrained as described (simulation 1) showed the presence of hydrophobic interactions of ligand side chains with Phe256, Val263, Ile829 and the hydrophobic part of Gln259 amino acid residues. Gln259 was

• α-amino group of Ile829 were obvious. The hydrophobic interactions were directed preferentially to Phe256, Val263, Leu260 and Ile829 residues and a hydrophobic part of Lys252. In contrast to simulation 1 with compound 1, there was no indication of compound 2 escaping from the SERCA cavity (Figure 4

Complexation of chiral amines by resorcin[4]arene sulfonic acids in polar media – circular dichroism and diffusion studies of chirality transfer and solvent dependence

• Bartosz Setner and
• Agnieszka Szumna

Beilstein J. Org. Chem. 2019, 15, 1913–1924, doi:10.3762/bjoc.15.187

• water [4][5]. Their cavities provide initial spatial constraints and prevent self-aggregation while hydrophobic interactions ensure thermodynamic gain. However, these restrictions alone are usually not sufficient to ensure the formation of complexes of a precise geometry. Seminal examples here are

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

• large variety of WMIs. To some of them, special names are assigned, such as hydrogen bonding or hydrophobic interactions. In chemistry, these WMIs are frequently used as if they were basic interaction types. For a long time, dispersion was largely ignored in chemistry, attractive intermolecular

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• pocket, the phenyl, the pyridine and the pyrimidine rings make critical hydrophobic interactions with residues in the shallow groove of the pocket [87]. Nearly simultaneously, the same group reported the SAR studies of a family of biphenylindole derivatives as inhibitors of the same PPI. A structure

Novel solid-phase strategy for the synthesis of ligand-targeted fluorescent-labelled chelating peptide conjugates as a theranostic tool for cancer

• Sagnik Sengupta,
• Mena Asha Krishnan,
• Premansh Dudhe,
• Ramesh B. Reddy,
• Bishnubasu Giri,
• Sudeshna Chattopadhyay and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2018, 14, 2665–2679, doi:10.3762/bjoc.14.244

• [42] of PSMA reveals that small molecule ligands such as DUPA would reach the PSMA active site through a gradually narrowing tunnel of amino acids of 20 Å length. Moreover, the inner surface of the PSMA tunnel possesses two hydrophobic pockets suitable for hydrophobic interactions with the amino acids

• present in the peptide spacer [38]. Therefore, it is pertinent to design a PSMA targeted conjugate that can pass through the tunnel smoothly and reach the active site as well as fit in hydrophobic pockets via hydrophobic interactions. Additionally, the carbonyl oxygen of the urea moiety of DUPA directly

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• two metal atoms in the binuclear active center via a water molecule in contrast to 2-ABA, where the carboxylate occupies this position (Figure 12). Moreover both, 2-ABA and the ligands 24–26 are stabilized by hydrophobic interactions. Additionally, compounds 24 and 25 are interacting with a histidine

• -inducer binding site in complex with 36 was solved at 2.95 Å resolution (Figure 16), as well as a co-crystal structure of the native HHQ C9-congener NHQ [76] demonstrating a competitive binding mode. When compared to the native ligand NHQ, 36 shows similar hydrophobic interactions (Figure 16). In addition

• hydrophobic interactions were observed in the tail region, in particular with leucins 189 and 208 as well as Y258. Mutations at these specific residues indicated that the π–π interactions of Y258 are crucial for M64's full inhibition with respect to pyocyanin production, which was only weakly inhibited in an

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

• vesicles composed of synthetic lipids and alkylated complexes of heptapropyl cobyrinate (Scheme 3) [32][33]. The alkylated B12 model complexes were introduced into the vesicle in aqueous solutions through non-covalent hydrophobic interactions and irradiated with a 500 W tungsten lamp to result in the

Synthesis of a water-soluble 2,2′-biphen[4]arene and its efficient complexation and sensitive fluorescence enhancement towards palmatine and berberine

• Xiayang Huang,
• Xinghua Zhang,
• Tianxin Qian,
• Junwei Ma,
• Lei Cui and
• Chunju Li

Beilstein J. Org. Chem. 2018, 14, 2236–2241, doi:10.3762/bjoc.14.198

• , respectively. π···π interactions, hydrophobic interactions and electrostatic attractions should play important roles in the association process. Although having similar structures, these two guests gave very different association constants. The substitution of 1,3-dioxole for two methoxy groups in P, affording

Synthesis and supramolecular self-assembly of glutamic acid-based squaramides

• Juan V. Alegre-Requena,
• Marleen Häring,
• Isaac G. Sonsona,
• Alex Abramov,
• Eugenia Marqués-López,
• Raquel P. Herrera and
• David Díaz Díaz

Beilstein J. Org. Chem. 2018, 14, 2065–2073, doi:10.3762/bjoc.14.180

• of a self-assembled network in organic solvents is likely driven by the formation of hydrogen bonds between different gelator molecules (polar head) as well as hydrophobic interactions between the long aliphatic chains. Considering our previous results obtained with diacids 1 and 2 [33], we initially

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

• performed by the dye micellization method using pyrene and eosin Y (EY) as fluorescent and spectrophotometric probes, respectively (Table 1). The nonpolar pyrene can be incorporated into hydrophobic domains of the aggregates due to hydrophobic interactions. Pyrene insertion is measured by analyzing the

• hydrophobic interactions with hydrophobic regions of calixarene aggregates that are typical for xanthene dyes [41]. The length of the alkyl chains in 10a,b does not affect the complex stoichiometry. Compounds 12a,b at concentrations below the CAC form dye–calixarene complexes of 2:1 stoichiometry [(X2

An amphiphilic pseudo[1]catenane: neutral guest-induced clouding point change

• Tomoki Ogoshi,
• Tomohiro Akutsu and
• Tada-aki Yamagishi

Beilstein J. Org. Chem. 2018, 14, 1937–1943, doi:10.3762/bjoc.14.167

• the cavity (Figure 4b), causing aggregation of the hydrophobic alkyl chain ring by hydrophobic interactions (Figure 4c). Conclusion We have successfully prepared a new amphiphilic bicyclic compound 3. A key feature of the molecule is that the hydrophobic part of the alkyl chain ring is hidden by

Efficient catenane synthesis by cucurbit[6]uril-mediated azide–alkyne cycloaddition

• Antony Wing Hung Ng,
• Chi-Chung Yee,
• Kai Wang and
• Ho Yu Au-Yeung

Beilstein J. Org. Chem. 2018, 14, 1846–1853, doi:10.3762/bjoc.14.158

• –ligand coordination, charge transfer, π-stacking and hydrophobic interactions, for the later interlocking of additional macrocycles to give higher-order [n]catenanes. The new building blocks were synthesized following similar procedures as previously described [24]. Catenane synthesis by CBAAC Synthesis

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

Hyper-reticulated calixarene polymers: a new example of entirely synthetic nanosponge materials

• Alberto Spinella,
• Marco Russo,
• Antonella Di Vincenzo,
• Delia Chillura Martino and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2018, 14, 1498–1507, doi:10.3762/bjoc.14.127

• efficiency indeed depends on the effective occurrence of both electrostatic and hydrophobic interactions between the guest and the polymer lattice. Thus, our CaNS nanosponges can be considered as a new class of purely synthetic smart absorbent materials. Keywords: calixarenes; nanosponges; smart materials

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• hydrophobic interactions (Figure 2). Figure 2a shows that the arginine side chain of the MATα2 N-terminal arm facilitates interaction between portions of the heterodimer MATα1–MATα2 with the minor groove of the DNA substrate by forming alternate H-bond interactions [25]. The main characteristic feature of

• ) was investigated in vitro by Shahabadi et al. by multispectroscopic techniques and molecular modeling study [108]. It has been shown that cytarabine acts in a groove-binding mode, which was confirmed by fluorescence experimental results of Hoechst 33258 displacement by the drug. Hydrophobic

• interactions play a crucial role in its binding to DNA groove. Similarly, the same group recently reported a macrocyclic copper(II) complex, ([CuL(ClO4)2] where L is 1,3,6,10,12,15-hexaazatricyclo[13.3.1.16,10]eicosane) and studied its interaction with calf thymus DNA (ct-DNA). It was confirmed that the Cu(II

Recent advances in synthetic approaches for medicinal chemistry of C-nucleosides

• Kartik Temburnikar and
• Katherine L. Seley-Radtke

Beilstein J. Org. Chem. 2018, 14, 772–785, doi:10.3762/bjoc.14.65

• modified nucleosides arise from changes in hydrogen bonding motifs, electronic effects, hydrophobic interactions, acid-base properties and chemical reactivity [25][26][27][28][29][30][31][32][33][34][35][36][37]. One such modification is the change in the nature of the glycosidic bond [29][37]. Although

Fluorogenic PNA probes

• Tirayut Vilaivan

Beilstein J. Org. Chem. 2018, 14, 253–281, doi:10.3762/bjoc.14.17

• interactions, it is mainly governed by hydrophobic interactions and hydrogen bonding between nucleobases and the GO surface [132]. Duplex DNA interacts less strongly with GO since the pairing nucleobases are buried inside the duplex in dsDNA. This phenomenon, together with the ability of GO to act as an

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• equivalent – methyl α-D-glucopyranoside – was investigated for a deeper understanding of the type of host–guest interactions. Solid state studies of PTX/CDs were performed using FTIR–ATR and Raman spectroscopy techniques. Keywords: antifolate; cyclodextrin; hydrophobic interactions; inclusion complexes

• phase. The hydrophobic interactions which are important stabilizing forces in solution are significantly diminished in the gas phase and do not manifest in the collisional experiments as it was concluded by the observation of increased gas-phase stability of γ-CD/FA complex comparing to its noncovalent

• directed inside the cavity are responsible for the formation of favorable hydrophobic interactions with the guest molecule. Similarly, H2 and H4 protons which are directed outwards the cavity may also interact, plausibly indirectly via OH hydrogen bonds, with guest molecules located outside the cavity. The

Towards open-ended evolution in self-replicating molecular systems

• Herman Duim and
• Sijbren Otto

Beilstein J. Org. Chem. 2017, 13, 1189–1203, doi:10.3762/bjoc.13.118

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• [45][56][57][58]. Prosperi and co-workers coated dodecanthiol AuNPs with manno-calixarenes exploiting hydrophobic interactions, obtaining an efficient targeting against cancer cells [56]. Similarly, a reversible addition−fragmentation chain transfer (RAFT) polymerization approach has been exploited

The effect of cyclodextrin complexation on the solubility and photostability of nerolidol as pure compound and as main constituent of cabreuva essential oil

• Joyce Azzi,
• Pierre-Edouard Danjou,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2017, 13, 835–844, doi:10.3762/bjoc.13.84

• hydrophobic interactions and that Ner penetrates the cavity from the wider side [28]. Furthermore, a ROESY experiment was performed to gain further insight into the dynamic structure of the β-CD/trans-Ner inclusion complex. The two-dimensional spectrum indicates a strong intermolecular cross-peaks between H3

Polyketide stereocontrol: a study in chemical biology

• Kira J. Weissman

Beilstein J. Org. Chem. 2017, 13, 348–371, doi:10.3762/bjoc.13.39

• hydrophobic interactions with the Tyr while being sterically accommodated by the relatively small Ser (Figure 7b). Finally, stereospecificity for the (2S)-isomer appears to lie in steric clashes that would occur between a (2R)-methyl group and both the Ser and His of the YASH motif. Nonetheless, efforts in