Correction to "Synthetic, Functional Thymidine-Derived Polydeoxyribonucleotide Analogues from a Six-Membered Cyclic Phosphoester".
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ABSTRACT:
SUBMITTER: Tsao YT
PROVIDER: S-EPMC8154422 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A grand challenge that crosses synthetic chemistry and biology is the scalable production of functional analogues of biomacromolecules. We have focused our attention on the use of deoxynucleoside building blocks bearing non-natural bases to develop a synthetic methodology that allows for the construction of high molecular weight deoxynucleotide polymers. Our six-membered cyclic phosphoester ring-opening polymerization strategy is demonstrated, herein, by an initial preparation of novel polyphosphoesters, comprised of butenyl-functionalized deoxyribonucleoside repeat units, connected via 3',5'-backbone linkages. A thymidine-derived bicyclic monomer, 3',5'-cyclic 3-(3-butenyl) thymidine ethylphosphate, was synthesized in two steps directly from thymidine, via butenylation and diastereoselective cyclization promoted by N,N-dimethyl-4-aminopyridine. Computational modeling of the six-membered 3',5'-cyclic phosphoester ring derived from deoxyribose indicated strain energies at least 5.4 kcal/mol higher than those of the six-membered monocyclic phosphoester, 2-ethoxy-1,3,2-dioxaphosphinane 2-oxide. These calculations supported the hypothesis that the strained 3',5'-cyclic monomer can promote ring-opening polymerization to afford the resulting poly(3',5'-cyclic 3-(3-butenyl) thymidine ethylphosphate)s with low dispersities (Đ < 1.10). This advanced design combines the merits of natural product-derived materials and functional, degradable polymers to provide a new platform for functional, synthetically derived polydeoxyribonucleotide-analogue materials.
| S-EPMC5451148 | biostudies-literature
Project description:The enantioselective copper-catalyzed oxidative coupling of alkenols with styrenes for the construction of dihydropyrans, isochromans, pyrans and morpholines is reported. A concise formal synthesis of a σ1 receptor ligand using this alkene carboetherification methodology was demonstrated. Ligand, solvent and base all impact reaction efficiency. DFT transition state calculations are presented.
| S-EPMC8590114 | biostudies-literature
Project description:The seven-membered cyclic potassium alumanyl species, [{SiNMes }AlK]2 [{SiNMes }={CH2 SiMe2 N(Mes)}2 ; Mes=2,4,6-Me3 C6 H2 ], which adopts a dimeric structure supported by flanking K-aryl interactions, has been isolated either by direct reduction of the iodide precursor, [{SiNMes }AlI], or in a stepwise manner via the intermediate dialumane, [{SiNMes }Al]2 . Although the intermediate dialumane has not been observed by reduction of a Dipp-substituted analogue (Dipp=2,6-i-Pr2 C6 H3 ), partial oxidation of the potassium alumanyl species, [{SiNDipp }AlK]2 , where {SiNDipp }={CH2 SiMe2 N(Dipp)}2 , provided the extremely encumbered dialumane [{SiNDipp }Al]2 . [{SiNDipp }AlK]2 reacts with toluene by reductive activation of a methyl C(sp3 )-H bond to provide the benzyl hydridoaluminate, [{SiNDipp }AlH(CH2 Ph)]K, and as a nucleophile with BPh3 and RN=C=NR (R=i-Pr, Cy) to yield the respective Al-B- and Al-C-bonded potassium aluminaborate and alumina-amidinate products. The dimeric structure of [{SiNDipp }AlK]2 can be disrupted by partial or complete sequestration of potassium. Equimolar reactions with 18-crown-6 result in the corresponding monomeric potassium alumanyl, [{SiNDipp }Al-K(18-cr-6)], which provides a rare example of a direct Al-K contact. In contrast, complete encapsulation of the potassium cation of [{SiNDipp }AlK]2 , either by an excess of 18-cr-6 or 2,2,2-cryptand, allows the respective isolation of bright orange charge-separated species comprising the 'free' [{SiNDipp }Al]- alumanyl anion. Density functional theory (DFT) calculations performed on this moiety indicate HOMO-LUMO energy gaps in the of order 200-250 kJ mol-1 .
| S-EPMC8596455 | biostudies-literature
Project description:Cidofovir (HPMPC, 1), a broad-spectrum antiviral agent, is currently used to treat AIDS-related human cytomegalovirus (HCMV) retinitis and has recognized therapeutic potential for orthopox virus infections, but is limited by its low oral bioavailability. Cyclic cidofovir (2) displays decreased nephrotoxicity compared to 1, while also exhibiting potent antiviral activity. Here we describe in detail the synthesis and evaluation as prodrugs of four cHPMPC dipeptide conjugates in which the free POH of 2 is esterified by the Ser side chain alcohol group of an X-L-Ser(OMe) dipeptide: 3 (X=L-Ala), 4 (X=L-Val), 5 (X=L-Leu), and 6 (X=L-Phe). Perfusion studies in the rat establish that the mesenteric permeability to 4 is more than 20-fold greater than to 1, and the bioavailability of 4 is increased 6-fold relative to 1 in an in vivo murine model. In gastrointestinal and liver homogenates, the cHPMPC prodrugs are rapidly hydrolyzed to 2. Prodrugs 3, 4, and 5 are nontoxic at 100 microM in HFF and KB cells and in cell-based plaque reduction assays had IC 50 values of 0.1-0.5 microM for HCMV and 10 microM for two orthopox viruses (vaccinia and cowpox). The enhanced transport properties of 3-6, conferred by incorporation of a biologically benign dipeptide moiety, and the facile cleavage of the Ser-O-P linkage suggest that these prodrugs represent a promising new approach to enhancing the bioavailability of 2.
| S-EPMC2629803 | biostudies-literature
Project description:The first synthesis, isolation, and characterization of permidin-2-ylidene complexes of Pd(II) is reported with entry resulting from either a direct reaction with isolable six-membered N-heterocyclic carbene or from the enetetramine, arising from dimerization of the carbene. Furthermore, a simplified method to prepare N,N'-disubstituted perimidinium bromide salts, precursors to 1,3-disubstituted perimidin-2-ylidene, was achieved using ammonium bromide as a source of weak acid. Through synthesis and nuclear magnetic resonance spectroscopic analysis of a carbene-phosphinidine adduct, an interrogation of the fundamental π-bonding ability of 1,3-diisopropylperimidin-2-ylidene revealed this interaction to be weak and of a similar order to unsaturated imidazol-2-ylidenes.
| S-EPMC6644826 | biostudies-literature
Project description:Two new crystal structures of eight- and ten-membered cyclic bis-anisyl-phosphono-thioyl disulfanes, namely 2,5-bis-(4-meth-oxy-phen-yl)-1,6,3,4,2λ5,5λ5-dioxadi-thiadi-phospho-cane-2,5-di-thione, C16H18O4P2S4, and 2,5-bis-(4-meth-oxy-phen-yl)-1,6,3,4,2λ5,5λ5-dioxadi-thia-diphosphecane-2,5-di-thione, C18H22O4P2S4, have been determined and compared to structures of the ferrocenyl analogues. The eight-membered rings have similar conformations (TBC) but the ten-membered macrocycles are differently puckered. Structural parameters of the relevant SPSSPS motif have been analysed and are discussed in detail. Compound 1 was refined as an inversion twin and 2 was refined as a two-component rotational twin.
| S-EPMC5956339 | biostudies-literature
Project description:The six-membered ring (SMR) is a common structure unit for numerous material systems. These materials include, but are not limited to, the typical two-dimensional materials such as graphene, h-BN, and transition metal dichalcogenides, as well as three-dimensional materials such as beryllium, magnesium, MgB2 and Bi2Se3. Although many of these materials have already become 'stars' in materials science and condensed-matter physics, little attention has been paid to the roles of the SMR unit across a wide range of compositions and structures. In this article, we systematically analyze these materials with respect to their very basic SMR structural unit, which has been found to play a deterministic role in the occurrence of many intriguing properties and phenomena, such as Dirac electronic and phononic spectra, superconductivity and topology. As a result, we have defined this group of materials as SMR inorganic materials, opening up a new perspective on materials research and development. With their unique properties, SMR materials deserve wide attention and in-depth investigation from materials design, new physical discoveries to target-wizard applications. It is expected that SMR materials will find niche applications in next-generation information technology, renewable energy, space, etc.
| S-EPMC8294346 | biostudies-literature
Project description:Thymidine analogues are powerful tools when studying DNA synthesis including DNA replication, repair and recombination. However, these analogues have been reported to have severe effects on cell-cycle progression and growth, the very processes being investigated in most of these studies. Here, we have analyzed the effects of 5-ethynyl-2'-deoxyuridine (EdU) and 5-Chloro-2'-deoxyuridine (CldU) using fission yeast cells and optimized the labelling procedure. We find that both analogues affect the cell cycle, but that the effects can be mitigated by using the appropriate analogue, short pulses of labelling and low concentrations. In addition, we report sequential labelling of two consecutive S phases using EdU and 5-bromo-2'-deoxyuridine (BrdU). Furthermore, we show that detection of replicative DNA synthesis is much more sensitive than DNA-measurements by flow cytometry.
| S-EPMC3923809 | biostudies-literature
Project description:Straightforward synthesis of cholesterol functionalized aliphatic N-substituted 8-membered cyclic carbonate (Chol-8m) monomer is reported. Well-defined poly(ethylene glycol) (PEG) diblock copolymers were readily accessed via organo catalytic ring opening polymerization. These polymers show promise as building blocks for self-assembled nanostructures and steric stabilizers for liposomes.
| S-EPMC7219653 | biostudies-literature
Project description:We design here new nanomolar antituberculotics, inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase (TMPKmt), by means of structure-based molecular design. 3D models of TMPKmt-inhibitor complexes have been prepared from the crystal structure of TMPKmt cocrystallized with the natural substrate deoxythymidine monophosphate (dTMP) (1GSI) for a training set of 15 thymidine analogues (TMDs) with known activity to prepare a QSAR model of interaction establishing a correlation between the free energy of complexation and the biological activity. Subsequent validation of the predictability of the model has been performed with a 3D QSAR pharmacophore generation. The structural information derived from the model served to design new subnanomolar thymidine analogues. From molecular modeling investigations, the agreement between free energy of complexation (??G com) and K i values explains 94% of the TMPKmt inhibition (pK i = -0.2924??G com + 3.234; R (2) = 0.94) by variation of the computed ??G com and 92% for the pharmacophore (PH4) model (pK i = 1.0206 × pK i (pred) - 0.0832, R (2) = 0.92). The analysis of contributions from active site residues suggested substitution at the 5-position of pyrimidine ring and various groups at the 5'-position of the ribose. The best inhibitor reached a predicted K i of 0.155?nM. The computational approach through the combined use of molecular modeling and PH4 pharmacophore is helpful in targeted drug design, providing valuable information for the synthesis and prediction of activity of novel antituberculotic agents.
| S-EPMC3619541 | biostudies-literature