Search results

Search for "binding" in Full Text gives 933 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.

Optimizations of lipid II synthesis: an essential glycolipid precursor in bacterial cell wall synthesis and a validated antibiotic target

  • Milandip Karak,
  • Cian R. Cloonan,
  • Brad R. Baker,
  • Rachel V. K. Cochrane and
  • Stephen A. Cochrane

Beilstein J. Org. Chem. 2024, 20, 220–227, doi:10.3762/bjoc.20.22

Graphical Abstract
  • study the mechanism of action of antimicrobial peptides that kill bacteria through binding to these polyprenyls [21][28][29][30][31][32][33][34]. Lipid II has been of particular interest, and during our synthesis of multiple different lipid II analogues, we have developed several optimizations, which we
  • in red and antimicrobial-binding motifs highlighted with blue arcs. R1 = H or Ac; R2 = H or Ac; R3 = OH, OMe or NH2; R4 = H or COOH; R5 = Gly5, Ala2, Ala-Ser/Ala or ᴅ-Asp; R6 = OH, OMe or NH2. These structural modifications are described in detail by Münch and co-workers [9]. For more details on
  • lipid II-binding antimicrobials, see recent review by Buijs and co-workers [2]. List of i) glycosyl donors and ii) glycosyl acceptors used in this study. Synthesis of disaccharide pentapeptide core 7. Synthesis of lipid II (11) and its analogues 8–10. Optimization of the glycosylation conditions.a
PDF
Album
Supp Info
Full Research Paper
Published 06 Feb 2024

Synthesis of the 3’-O-sulfated TF antigen with a TEG-N3 linker for glycodendrimersomes preparation to study lectin binding

  • Mark Reihill,
  • Hanyue Ma,
  • Dennis Bengtsson and
  • Stefan Oscarson

Beilstein J. Org. Chem. 2024, 20, 173–180, doi:10.3762/bjoc.20.17

Graphical Abstract
  • (β-ᴅ-GalNAc-(1→4)-β-ᴅ-GlcNAc), which have then been used for production of the glycodenrimersomes and interaction studies with various galectins [1][2]. In the continuation of this collaboration, to investigate the binding of siglec-1 and the chimera of 3’-SuTF-binding siglecs and TF-binding galectin
PDF
Album
Supp Info
Full Research Paper
Published 30 Jan 2024

Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[c]quinolizinium ions

  • Julika Schlosser,
  • Olga Fedorova,
  • Yuri Fedorov and
  • Heiko Ihmels

Beilstein J. Org. Chem. 2024, 20, 101–117, doi:10.3762/bjoc.20.11

Graphical Abstract
  • organic solvents (78–20% in MeCN). The quinolizinium derivatives bind to DNA by intercalation with binding constants of 6–11 × 104 M−1, as shown by photometric and fluorimetric titrations as well as by CD- and LD-spectroscopic analyses. These ligand–DNA complexes can also be established in situ upon
  • irradiation of the styrylpyridines and formation of the intercalator directly in the presence of DNA. In addition to the DNA-binding properties, the tested benzo[c]quinolizinium derivatives also operate as photosensitizers, which induce DNA damage at relative low concentrations and short irradiation times
  • a change of the DNA structure or occupy binding sites of essential enzymes, which in turn may influence or even inhibit important biochemical processes, for example DNA replication or transcription [1][2]. As a result, the development of DNA-targeting drugs still involves the design of suitable DNA
PDF
Album
Supp Info
Full Research Paper
Published 18 Jan 2024

Aldiminium and 1,2,3-triazolium dithiocarboxylate zwitterions derived from cyclic (alkyl)(amino) and mesoionic carbenes

  • Nedra Touj,
  • François Mazars,
  • Guillermo Zaragoza and
  • Lionel Delaude

Beilstein J. Org. Chem. 2023, 19, 1947–1956, doi:10.3762/bjoc.19.145

Graphical Abstract
  • of charges (Figure 1) [13][14][15][16]. Crabtree and co-workers first reported the abnormal binding of an imidazolium salt to an iridium hydride at the C4 carbon atom instead of C2 in 2001 [17][18]. Since then, many other metal complexes bearing imidazol-4-ylidene ligands (F) have been reported [7
PDF
Album
Supp Info
Full Research Paper
Published 20 Dec 2023

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

  • Mateusz Marcisz,
  • Sebastian Anila,
  • Margrethe Gaardløs,
  • Martin Zacharias and
  • Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

Graphical Abstract
  • essential to explain their biological functions. In this study, the umbrella sampling (US) approach is used to pull away a GAG ligand from the binding site and then pull it back in. We analyze the binding interactions between GAGs of three types (heparin, desulfated heparan sulfate, and chondroitin sulfate
  • GAG properties, especially protein recognition specificity and multipose binding. We found that the binding free energy landscape in the proximity of the GAG native binding pose is complex and implies the co-existence of several binding poses. The sliding of a GAG chain along a protein surface could
  • to multipose binding, wherein various configurations of the protein–GAG complex may exhibit similar free binding energies, allowing them to co-exist. Interpreting the “sulfation code”, the amount (net sulfation) and particular positions of the sulfation group (sulfation pattern), could assist in the
PDF
Album
Supp Info
Full Research Paper
Published 19 Dec 2023

Anion–π catalysis on carbon allotropes

  • M. Ángeles Gutiérrez López,
  • Mei-Ling Tan,
  • Giacomo Renno,
  • Augustina Jozeliūnaitė,
  • J. Jonathan Nué-Martinez,
  • Javier Lopez-Andarias,
  • Naomi Sakai and
  • Stefan Matile

Beilstein J. Org. Chem. 2023, 19, 1881–1894, doi:10.3762/bjoc.19.140

Graphical Abstract
  • formation (Figure 1C) [12]. This intriguing mechanism of catalysis should be further intensified on single-walled carbon nanotubes 2 (SWCNTs, Figure 1D) and multi-walled carbon nanotubes 3 (MWCNTs, Figure 1E) [13]. Multiple substrate/transition-state binding should reduce particularly in-plane polarization
  • of the π system and thus induced anion–π interactions. Since the polarization caused by substrate/transition-state binding hinders additional binding, this effect should occur only at high concentrations. These expectations were first explored with anion–π catalysis on fullerenes in 2017 [12
  • -to-face π stacking because the delocalized π electrons move within the stack away from the charge, which induces a macrodipole along the stack that supports the binding of the anion (Figure 1B) [61]. What works for anion–(π)n–π catalysis on π-stacked foldamers [61] and micelles [8] should apply to
PDF
Album
Review
Published 12 Dec 2023

N-Boc-α-diazo glutarimide as efficient reagent for assembling N-heterocycle-glutarimide diads via Rh(II)-catalyzed N–H insertion reaction

  • Grigory Kantin,
  • Pavel Golubev,
  • Alexander Sapegin,
  • Alexander Bunev and
  • Dmitry Dar’in

Beilstein J. Org. Chem. 2023, 19, 1841–1848, doi:10.3762/bjoc.19.136

Graphical Abstract
  • , using a new synthesis strategy based on the usage of diazo glutarimide 4 (Scheme 1). Compared to thalidomide (Figure 1), the resulting “benzotriazolo thalidomide” has a similar binding mode, but improved properties, as revealed in crystallographic analyses, affinity assays and cell culture [26]. However
PDF
Album
Supp Info
Full Research Paper
Published 07 Dec 2023

Quinoxaline derivatives as attractive electron-transporting materials

  • Zeeshan Abid,
  • Liaqat Ali,
  • Sughra Gulzar,
  • Faiza Wahad,
  • Raja Shahid Ashraf and
  • Christian B. Nielsen

Beilstein J. Org. Chem. 2023, 19, 1694–1712, doi:10.3762/bjoc.19.124

Graphical Abstract
  • separation by reducing Coulomb attraction and exciton binding energy. The resulting enhancement in exciton dissociation and reduced charge recombination contribute to the improved performance of polymer acceptors, especially Qx2 which achieved PCE of 5.32% with PBDB-T donor in an all-PSC device [20]. In a
PDF
Album
Review
Published 09 Nov 2023

Tying a knot between crown ethers and porphyrins

  • Maksym Matviyishyn and
  • Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

Graphical Abstract
  • binding guest molecules/ions, but also to undergo unusual transformations, such as metal-induced expansion/contraction. Depending on the design of the particular hybrid, they present unique features involving intriguing redox chemistry, interesting optical properties, and reactivity towards transition
  • date back to 1982 when Krishnan and Thanabal reported synthesising a new host molecule with multiple cavities capable of encompassing several guest molecules/ions [39]. The molecule demonstrated an exciting feature of binding Na+, Mg2+, Ca2+, K+, NH4+, and Ba2+ cations. The incorporation of cations
  • [46]. The macrotetracycles and macropentacycles, apart from the apparent metal complexation within the porphyrin core, showed cationic guest binding upon adding different ammonium salts, forming 1:1 complexes. Later, in 1985, Camilleri and co-workers reported the synthesis of a capped porphyrin
PDF
Album
Perspective
Published 27 Oct 2023
Graphical Abstract
  • the amine nitrogen of the guest molecule. In addition to hydrogen bonding, other interactions such as π–π stacking and electrostatic interactions also play a role in the complexation process. These interactions can be modulated by changing the pH, solvent, and temperature of the solution. The binding
  • affinity and selectivity of the R[4]A–amine complexes depend on several factors, including the size, shape, and functional groups of both the host and the guest molecules. For example, R[4]A derivatives with different substituents on the aromatic rings [12] have been synthesized to enhance the binding
  • dipropylamine and diisopropylamine, complexes with a stoichiometry of 1:2 are formed (i.e., 1 molecule of R[4]A binding to 2 molecules of dipropylamine or diisopropylamine). Regardless of the quantity of amine added to the solution of R[4]A in ethanol (4 equiv, 2 equiv, and 1 equiv, respectively), a 1:2
PDF
Album
Supp Info
Full Research Paper
Published 29 Sep 2023

Synthesis and biological evaluation of Argemone mexicana-inspired antimicrobials

  • Jessica Villegas,
  • Bryce C. Ball,
  • Katelyn M. Shouse,
  • Caleb W. VanArragon,
  • Ashley N. Wasserman,
  • Hannah E. Bhakta,
  • Allen G. Oliver,
  • Danielle A. Orozco-Nunnelly and
  • Jeffrey M. Pruet

Beilstein J. Org. Chem. 2023, 19, 1511–1524, doi:10.3762/bjoc.19.108

Graphical Abstract
  • often attributed to high binding affinity to DNA, interference with protein biosynthesis, induction of membrane leakage, and affecting GTPase activity in bacteria cell division [12][13][14][15]. Recent reports have also pointed to inhibition of the ‘filamenting temperature-sensitive mutant Z’ (FtsZ
  • ) protein [16][17], as well as perturbing carbohydrate metabolism to generate reactive oxygen species that damage the DNA [18], as modes of action for berberine’s antibacterial effects. The antitumor properties of berberine have been attributed to DNA binding, and in particular regulating the activity of
PDF
Album
Supp Info
Full Research Paper
Published 29 Sep 2023

Application of N-heterocyclic carbene–Cu(I) complexes as catalysts in organic synthesis: a review

  • Nosheen Beig,
  • Varsha Goyal and
  • Raj K. Bansal

Beilstein J. Org. Chem. 2023, 19, 1408–1442, doi:10.3762/bjoc.19.102

Graphical Abstract
  • ), bear only a single flanking heteroatom and exist as a zwitterionic structure with no neutral canonical resonance form (Figure 3). In this case, binding takes place via the C4 or C5 position. These NHCs have been found to be stronger electron-donors due to the reduced σ-withdrawal from the carbene carbon
  • 1,3-dipolar cycloaddition and belongs to the general category of [π4s + π2s] cycloadditions. It is an important method to construct a five-membered heterocyclic ring [66]. As discussed earlier, the Cu atom in NHC–Cu(I) complexes has nucleophilic character, which allows binding to the positive end of
  • -donors on the catalytic activity of NHC–Cu(I) complexes for azide–alkyne [3 + 2] cycloaddition reactions [67]. They determined binding constants of four NHC–CuCl complexes with two N-donors, which revealed that addition of phenanthroline to the NHC–CuCl enhanced the catalytic activity manifold. In fact
PDF
Album
Review
Published 20 Sep 2023

Synthesis of ether lipids: natural compounds and analogues

  • Marco Antônio G. B. Gomes,
  • Alicia Bauduin,
  • Chloé Le Roux,
  • Romain Fouinneteau,
  • Wilfried Berthe,
  • Mathieu Berchel,
  • Hélène Couthon and
  • Paul-Alain Jaffrès

Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96

Graphical Abstract
  • ). The review of Lemaire et al., dedicated to the synthesis of glycerol ether, is complemental to this review article [57]. Of note, the review of Godfroid and Braquet attempted to decipher the binding site of PAF via a QSAR study [58]. 1.1 Synthesis of PAF and some building blocks The platelet
PDF
Album
Review
Published 08 Sep 2023

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

  • Carlee A. Montgomery and
  • Graham K. Murphy

Beilstein J. Org. Chem. 2023, 19, 1171–1190, doi:10.3762/bjoc.19.86

Graphical Abstract
  • numerous similar attributes, halogen bonding has also proven to be a viable alternative in methodologies that rely on hydrogen bond initiation. For example, both halogen- and hydrogen bonding can be used in supramolecular chemistry as the binding mechanism in photoresponsive receptors [73][74][75][76][77
  • . used 1H NMR titrations and isothermal titration calorimetry (ITC) to experimentally determine interactions energies for I-9 complexes (e.g., I-9-lig, −6.3 kcal/mol), they also discovered that simultaneous binding to both σ-holes was possible [90]. Given these observations, it is unsurprising that HVI
PDF
Album
Review
Published 07 Aug 2023

CO2 complexation with cyclodextrins

  • Cecilie Høgfeldt Jessen,
  • Jesper Bendix,
  • Theis Brock Nannestad,
  • Heloisa Bordallo,
  • Martin Jæger Pedersen,
  • Christian Marcus Pedersen and
  • Mikael Bols

Beilstein J. Org. Chem. 2023, 19, 1021–1027, doi:10.3762/bjoc.19.78

Graphical Abstract
  • , are studied as potential CO2 capture agents due to their unique molecular structures and high selectivity towards CO2. In this paper we have investigated binding efficiency of a number of cyclodextrins towards CO2. It is found that the crystal structure of α-cyclodextrin with CO2 has a 1:1
  • stoichioimetry and that a number of simple and modified cyclodextrins bind CO2 in water with a Kg of 0.18–1.2 bar−1 (7–35 M−1) with per-O-methyl α-cyclodextrin having the highest CO2 affinity. Keywords: carbon dioxide; crystals; cyclodextrin; gas binding; Introduction The concentration of carbon dioxide (CO2
  • CO2 is captured by non-covalent binding. Henglein and Cramer showed many years ago that α-cyclodextrin (1, Figure 1), when treated with CO2 under pressure for several days gave crystals with the gas trapped inside [8]. According to Cramer only 1 was able to form crystals, while larger cyclodextrins
PDF
Album
Supp Info
Full Research Paper
Published 17 Jul 2023

Intermediates and shunt products of massiliachelin biosynthesis in Massilia sp. NR 4-1

  • Till Steinmetz,
  • Blaise Kimbadi Lombe and
  • Markus Nett

Beilstein J. Org. Chem. 2023, 19, 909–917, doi:10.3762/bjoc.19.69

Graphical Abstract
  • chelate environmental Fe3+. Ligand groups, such as hydroxamate, phenolate, catecholate, carboxylate, or oxazoline/thiazoline residues, confer siderophores their high affinity for the binding of Fe3+ [3][4][5]. Following the coordination of the metal, the Fe3+-loaded siderophore complex is transported back
PDF
Album
Supp Info
Full Research Paper
Published 23 Jun 2023

A fluorescent probe for detection of Hg2+ ions constructed by tetramethyl cucurbit[6]uril and 1,2-bis(4-pyridyl)ethene

  • Xiaoqian Chen,
  • Naqin Yang,
  • Yue Ma,
  • Xinan Yang and
  • Peihua Ma

Beilstein J. Org. Chem. 2023, 19, 864–872, doi:10.3762/bjoc.19.63

Graphical Abstract
  • detection of heavy metal ions. Results and Discussion The interactions of G with TMeQ[6] UV–vis spectroscopy analysis The binding interaction between G and TMeQ[6] in aqueous solution was studied using UV–vis absorption spectroscopy. Figure 2a shows that the absorbance of G decreases with the addition of
  • TMeQ[6], and the wavelength redshifts from 301 nm to 330 nm, indicating that TMeQ[6] has binding affinity for G. The molar ratio method (Figure 2b) shows that when n(TMeQ[6])/n(G) = 1:1, the absorption value of the system gradually stabilizes, indicating that the guest G and TMeQ[6] form an inclusion
  • , which is an exothermic reaction (enthalpy-driven). The results show that the binding ability of G and TMeQ[6] is strong, and the ratio is 1:1. The results are consistent with those obtained by UV–vis spectroscopy and fluorescence spectroscopy. Single-crystal X-ray diffraction analysis The crystal
PDF
Album
Supp Info
Full Research Paper
Published 13 Jun 2023

pH-Responsive fluorescent supramolecular nanoparticles based on tetraphenylethylene-labelled chitosan and a six-fold carboxylated tribenzotriquinacene

  • Nan Yang,
  • Yi-Yan Zhu,
  • Wei-Xiu Lin,
  • Yi-Long Lu and
  • Wen-Rong Xu

Beilstein J. Org. Chem. 2023, 19, 635–645, doi:10.3762/bjoc.19.45

Graphical Abstract
  • -soluble bowl-shaped six-fold carboxylated tribenzotriquinacene derivative TBTQ-C6 via host–guest binding. The spherical nanoparticles formed by CS-TPE amphiphiles or TBTQ-C6/CS-TPE supra-amphiphiles disintegrated under alkaline stimulation at pH 10.4 and the dispersion of the aggregates after the collapse
  • construct pH-responsive supramolecular vesicles and molecule-scale drug carriers, respectively. Both of them exhibited pH-responsive properties, with the host–guest binding disintegrating when the pH of the solution is adjusted to 5.5 and the binding regenerated when the pH is restored to 7.4. These
  • structures. As shown in Figure 7b, the emission of all CS-TPE in a solution at pH 5.3 was enhanced after the addition of the host TBTQ-C6. This effect can be attributed to the further inhibition of the intramolecular rotation of the phenyl rings of TPE after binding with the host molecule [31]. The
PDF
Album
Supp Info
Full Research Paper
Published 08 May 2023

C3-Alkylation of furfural derivatives by continuous flow homogeneous catalysis

  • Grédy Kiala Kinkutu,
  • Catherine Louis,
  • Myriam Roy,
  • Juliette Blanchard and
  • Julie Oble

Beilstein J. Org. Chem. 2023, 19, 582–592, doi:10.3762/bjoc.19.43

Graphical Abstract
  • Supporting Information File 1, p. S20), meaning that the ruthenium trimer was no longer present. The TEM analysis of the recovered solid phase (Scheme 5B) showed the formation of large aggregates with high electron density. Moreover, ruthenium was detected by XPS analysis (Scheme 5B); the binding energy of
PDF
Album
Supp Info
Full Research Paper
Published 03 May 2023

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

Graphical Abstract
  • exhibited a micromolar and submicromolar binding affinity for ds-polynucleotides and inactivated a mutant of dipeptidyl peptidase enzyme E451A. Confocal microscopy revealed that the conjugate with the longer linker entered the HeLa cell membranes and blue fluorescence was visualized as the dye accumulated
  • RNA, single or double-stranded polynucleotides, particular base composition…) and signalize binding by specific spectroscopic response is of great importance [1][2]. Pyrene derivatives are among the earliest known fluorescent probes for biomolecules. These chromophores are often used due to their high
  • extinction coefficient and long emission lifetime (>100 ns) [3]. Their large aromatic hydrophobic surface allows the intercalation between DNA/RNA base pairs and binding within the minor groove. Pyrenes are also prominent protein probes that can monitor protein conformational changes because of pyrene
PDF
Album
Supp Info
Full Research Paper
Published 26 Apr 2023

Dipeptide analogues of fluorinated aminophosphonic acid sodium salts as moderate competitive inhibitors of cathepsin C

  • Karolina Wątroba,
  • Małgorzata Pawełczak and
  • Marcin Kaźmierczak

Beilstein J. Org. Chem. 2023, 19, 434–439, doi:10.3762/bjoc.19.33

Graphical Abstract
  • pocket of the enzyme. In contrast, the S2 pocket preferably accommodates amino acids having short aliphatic side-chains, but also recognizes aromatic amino acids, preferably phenylalanine. To study the structural requirements of the S1 binding site of the enzyme, we synthesized a series of ten dipeptide
PDF
Album
Supp Info
Full Research Paper
Published 12 Apr 2023

Combretastatins D series and analogues: from isolation, synthetic challenges and biological activities

  • Jorge de Lima Neto and
  • Paulo Henrique Menezes

Beilstein J. Org. Chem. 2023, 19, 399–427, doi:10.3762/bjoc.19.31

Graphical Abstract
  • . After binding to tubulin, they act as stabilizing agents, allowing the formation of microtubules in the early stages, but preventing their disassembly in the final stages of cell division, thus leading to apoptosis [15][55][74] in a mechanism similar to taxol® [76]. However, it is worth to note that
PDF
Album
Review
Published 29 Mar 2023

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

  • Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

Graphical Abstract
  • carbohydrate sequences suitable for tumor-binding-associated lectins on the porphyrin periphery. Continuing our work on the functionalization of porphyrin at the meso-position [32][33], we used the CuAAC click protocol to synthesize meso-phenyltriazole-linked porphyrin-coumarin dyads 44–48 in good to excellent
  • % yield using Cu(MeCN)4PF6 and triethylamine in anhydrous DMF. This ‘capped’ porphyrin was designed so that the rigid triazole linkers prevent the capping group from collapsing onto the porphyrin. Gilday et al. [60] also synthesized porphyrin 142 and studied its anion-binding properties and found that it
  • has very strong anion-binding affinities for various anions. In 2019, Ol’shevskaya [61] and co-workers synthesized meso-tetratriazole-bridged fluorinated porphyrin-maleimine conjugates 145a–c in 54–58% yields by using the CuAAC reaction between azidoporphyrins 143a,b and N-propargylmaleimide (144) in
PDF
Album
Review
Published 22 Mar 2023

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

  • Robert N. Goldberg,
  • Robert T. Giessmann,
  • Peter J. Halling,
  • Carsten Kettner and
  • Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

Graphical Abstract
  • (overall) biochemical reaction involves sums of species that differ only in protonation and, if present, Mg2+ and Ca2+ binding states. It has an equilibrium constant K’, which is referred to as an “apparent equilibrium constant” [10]. A biochemical reaction should be carried out at essentially a constant
  • equilibrium. The total ATP concentration is the sum of the concentrations of the individual ionic species formed by the protonation or metal ion binding reactions of the ATP species Additional metal ion complexes (e.g., involving Ca2+, K+, and Na+) can also be included in Equation 4. Similar expressions can
  • examples are Note that different numbers of protons are shown on the right-hand side of Equations 5, 6, and 7. Thus, the change in binding ΔrN(H+) = 1 for Equation 5, but ΔrN(H+) = 2 and 0 for Equation 6 and Equation 7, respectively. The overall biochemical Equation 1 is, in fact, an ensemble of many
PDF
Album
Perspective
Published 15 Mar 2023

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

Graphical Abstract
  • derivatives in this study were modeled in the neutral form (despite their pKa values in aqueous solution may be higher than 7). Superimposing the binding pose of the most potent inhibitor 29 in the active site of dGMII on the bound swainsonine in the X-ray complex (PDB ID: 3BLB) [23][39] (Figure 2) showed
  • bonds with the side chains of Tyr727 and Asp472 [d(C5-OH···Tyr727-OH) = 1.48 Å, and d(C5-OH···Asp472-COO−) = 1.55 Å, BP86/LACVP*:OPLS2005] and interacts with the hydrophobic pocket created by Tyr727, Phe206 and Trp415. Also, the binding position of this side chain is in a good overlap with the
  • the binding pose of the lyxitol core in 28 compared to 29 and a subsequent weakening in ΔEring-E (from −514.35 kcal mol−1 in 29 to −502.70 kcal mol−1 in 28), which is the major component of the overall interaction energy between the inhibitor and the enzyme. This assumption was further supported by
PDF
Album
Supp Info
Full Research Paper
Published 06 Mar 2023
Other Beilstein-Institut Open Science Activities