Triplex Forming Oligonucleotide Reagents: Rationalization of DNA Site Selectivity and Application in a Pharmaceutical Context

1990 ◽  
pp. 565-578 ◽  
Author(s):  
Ross H. Durland ◽  
Donald J. Kessler ◽  
Madeleine Duvic ◽  
Michael Hogan
Keyword(s):  
Site Selectivity ◽  
Triplex Forming Oligonucleotide

Chelation-assisted transition metal-catalysed C–H chalcogenylations

2020 ◽  
Vol 7 (8) ◽  
pp. 1022-1060 ◽  
Author(s):  
Wenbo Ma ◽  
Nikolaos Kaplaneris ◽  
Xinyue Fang ◽  
Linghui Gu ◽  
Ruhuai Mei ◽  
...  
Keyword(s):  
Transition Metal ◽  
Recent Advances ◽  
Site Selectivity ◽  
Transition Metal Catalyzed ◽  
Metal Catalyzed

This review summarizes recent advances in C–S and C–Se formations via transition metal-catalyzed C–H functionalization utilizing directing groups to control the site-selectivity.

Cobalt/Lewis Acid Catalysis for Hydrocarbofunctionalization of Alkynes via Cooperative C–H Activation

2020 ◽  
Author(s):  
Chang-Sheng Wang ◽  
Sabrina Monaco ◽  
Anh Ngoc Thai ◽  
Md. Shafiqur Rahman ◽  
Chen Wang ◽  
...  
Keyword(s):  
Catalytic System ◽  
Lewis Acid ◽  
Hydrogen Transfer ◽  
Acid Catalysis ◽  
Rate Limiting Step ◽  
Site Selectivity ◽  
Set Up ◽  
Site Selective ◽  
First Time ◽  
Rate Limiting

A catalytic system comprised of a cobalt-diphosphine complex and a Lewis acid (LA) such as AlMe3 has been found to promote hydrocarbofunctionalization reactions of alkynes with Lewis basic and electron-deficient substrates such as formamides, pyridones, pyridines, and azole derivatives through site-selective C-H activation. Compared with known Ni/LA catalytic system for analogous transformations, the present catalytic system not only feature convenient set up using inexpensive and bench-stable precatalyst and ligand such as Co(acac)3 and 1,3-bis(diphenylphosphino)propane (dppp), but also display distinct site-selectivity toward C-H activation of pyridone and pyridine derivatives. In particular, a completely C4-selective alkenylation of pyridine has been achieved for the first time. Mechanistic stidies including DFT calculations on the Co/Al-catalyzed addition of formamide to alkyne have suggested that the reaction involves cleavage of the carbamoyl C-H bond as the rate-limiting step, which proceeds through a ligand-to-ligand hydrogen transfer (LLHT) mechanism leading to an alkyl(carbamoyl)cobalt intermediate.

Imine as a Linchpin Approach for Distal C(sp2)–H Functionalization

2020 ◽  
Author(s):  
Sukdev Bag ◽  
Sadhan Jana ◽  
Sukumar Pradhan ◽  
Suman Bhowmick ◽  
Nupur Goswami ◽  
...  
Keyword(s):  
Organic Molecules ◽  
Bond Activation ◽  
Bond Formation ◽  
Ancillary Ligand ◽  
Significant Challenge ◽  
Site Selectivity ◽  
Directing Group ◽  
Covalently Linked ◽  
Complex Organic ◽  
Post Functionalization

<p>Despite the widespread applications of C–H functionalization, controlling site selectivity remains a significant challenge. Covalently attached directing group (DG) served as an ancillary ligand to ensure proximal <i>ortho</i>-, distal <i>meta</i>- and <i>para</i>-C-H functionalization over the last two decades. These covalently linked DGs necessitate two extra steps for a single C–H functionalization: introduction of DG prior to C–H activation and removal of DG post-functionalization. We introduce here a transient directing group for distal C(<i>sp<sup>2</sup></i>)-H functionalization <i>via</i> reversible imine formation. By overruling facile proximal C-H bond activation by imine-<i>N</i> atom, a suitably designed pyrimidine-based transient directing group (TDG) successfully delivered selective distal C-C bond formation. Application of this transient directing group strategy for streamlining the synthesis of complex organic molecules without any necessary pre-functionalization at the distal position has been explored.</p>

Theoretical and experimental studies of palladium-catalyzed site-selective C(sp3)−H bond functionalization enabled by transient ligands

2017 ◽  
Author(s):  
Haibo Ge ◽  
Lei Pan ◽  
Piaoping Tang ◽  
Ke Yang ◽  
Mian Wang ◽  
...  
Keyword(s):  
Bond Activation ◽  
Theoretical Calculations ◽  
Experimental Studies ◽  
Bond Functionalization ◽  
Aliphatic Ketones ◽  
Site Selectivity ◽  
Mechanistic Investigation ◽  
Palladium Catalyzed ◽  
Metal Catalyzed ◽  
Site Selective

Transition metal-catalyzed selective C–H bond functionalization enabled by transient ligands has become an extremely attractive topic due to its economical and greener characteristics. However, catalytic pathways of this reaction process on unactivated sp<sup>3</sup> carbons of reactants have not been well studied yet. Herein, detailed mechanistic investigation on Pd-catalyzed C(sp<sup>3</sup>)–H bond activation with amino acids as transient ligands has been systematically conducted. The theoretical calculations showed that higher angle distortion of C(sp2)-H bond over C(sp3)-H bond and stronger nucleophilicity of benzylic anion over its aromatic counterpart, leading to higher reactivity of corresponding C(sp<sup>3</sup>)–H bonds; the angle strain of the directing rings of key intermediates determines the site-selectivity of aliphatic ketone substrates; replacement of glycine with β-alanine as the transient ligand can decrease the angle tension of the directing rings. Synthetic experiments have confirmed that β-alanine is indeed a more efficient transient ligand for arylation of β-secondary carbons of linear aliphatic ketones than its glycine counterpart.<br><br>

Antigene and Antiproliferative Effects of Triplex-Forming Oligonucleotide (TFO) Targeted on hmgb1 Gene in Human Hepatoma Cells

2020 ◽  
Vol 20 (16) ◽  
pp. 1943-1955
Author(s):  
Neelam Lohani ◽  
Moganty R. Rajeswari
Keyword(s):  
Apoptotic Cell ◽  
Isothermal Calorimetry ◽  
High Mobility ◽  
Rational Drug Design ◽  
Human Hepatoma Cells ◽  
Aberrant Expression ◽  
Bioinformatic Tools ◽  
Hmgb1 Expression ◽  
Dna Triplex ◽  
Triplex Forming Oligonucleotide

Background: The high mobility group box 1 (hmgb1) is one of the frequently over-expressed genes whose aberrant expression is reported in a number of human cancers. Various strategies are underway to inhibit hmgb1 expression in cancer cells having considerable therapeutic value. Objective: The present work involves selective transcriptional inhibition of the hmgb1 gene using selective DNA triplex structure-based gene technology. Here, the promoter region of the hmgb1 gene at position (-183 to -165) from the transcription start site as a target was selected using bioinformatic tools. Methods: The DNA triplex formation by the DNA of the target gene and TFO was confirmed using UV absorption spectroscopy, Circular Dichroism, and Isothermal Calorimetry. Results: Treatment of HepG2 cell with specific Triplex-forming Oligonucleotide significantly downregulated HMGB1 expression level at mRNA and protein levels by 50%, while the classical anticancer drugs, actinomycin/ adriamycin as positive controls showed 65% and the combination of TFO and drug decreased by 70%. The anti-proliferative effects of TFO correlated well with the fact of accumulation of cells in the Go phase and apoptotic cell death. Further, the binding of anti-cancer drugs to hmgb1 is stronger in DNA triplex state as compared to hmgb1 alone, suggesting the combination therapy as a better option. Conclusion: Therefore, the ability of hmgb1 targeted triplex-forming oligonucleotide in combination with triplex selective anticancer drug holds promise in the treatment of malignancies associated with hmgb1 overexpression. The result obtained may open up new vistas to provide a basis for the rational drug design and searching for high-affinity ligands with a high triplex selectivity.

scholarly journals Reconstructing the Free Energy Profiles Describing the Switching Mechanism of a pH-Dependent DNA Nanodevice from ABMD Simulations

2021 ◽  
Vol 11 (9) ◽  
pp. 4052
Author(s):  
Alice Romeo ◽  
Mattia Falconi ◽  
Alessandro Desideri ◽  
Federico Iacovelli
Keyword(s):  
Free Energy ◽  
Double Helix ◽  
Minimum Energy ◽  
Switching Mechanism ◽  
Linker Length ◽  
Energy Profiles ◽  
Functional Dna ◽  
Triplex Forming Oligonucleotide ◽  
Dynamics Simulations ◽  
Free Energy Profiles

The pH-responsive behavior of six triple-helix DNA nanoswitches, differing in the number of protonation centers (two or four) and in the length of the linker (5, 15 or 25 bases), connecting the double-helical region to the single-strand triplex-forming region, was characterized at the atomistic level through Adaptively Biased Molecular Dynamics simulations. The reconstruction of the free energy profiles of triplex-forming oligonucleotide unbinding from the double helix identified a different minimum energy path for the three diprotic nanoswitches, depending on the length of the connecting linker and leading to a different per-base unbinding profile. The same analyses carried out on the tetraprotic switches indicated that, in the presence of four protonation centers, the unbinding process occurs independently of the linker length. The simulation data provide an atomistic explanation for previously published experimental results showing, only in the diprotic switch, a two unit increase in the pKa switching mechanism decreasing the linker length from 25 to 5 bases, endorsing the validity of computational methods for the design and refinement of functional DNA nanodevices.

Crossover Site-Selectivity in the Adsorption of the Fullerene Derivative PCBM on Au(111)

2007 ◽  
Vol 46 (41) ◽  
pp. 7874-7877 ◽  
Author(s):  
David Écija ◽  
Roberto Otero ◽  
Luis Sánchez ◽  
José María Gallego ◽  
Yang Wang ◽  
...  
Keyword(s):  
Fullerene Derivative ◽  
Site Selectivity ◽  
Crossover Site

A new synthetic analogue of the bracken ultimate carcinogen: Elevation of stability and alteration of DNA alkylation site selectivity

1997 ◽  
Vol 38 (18) ◽  
pp. 3235-3238 ◽  
Author(s):  
Hideo Kigoshi ◽  
Yuusi Kitamura ◽  
Tatsuya Fujita ◽  
Hidekazu Ohashi ◽  
Toshiyuki Atsumi ◽  
...  
Keyword(s):  
Dna Alkylation ◽  
Synthetic Analogue ◽  
Site Selectivity

Remote C–H Functionalizations by Ruthenium Catalysis

Synthesis ◽  
2021 ◽  
Author(s):  
Korkit Korvorapun ◽  
Ramesh C. Samanta ◽  
Torben Rogge ◽  
Lutz Ackermann
Keyword(s):  
Steric Hindrance ◽  
Late Stage ◽  
Crop Protection ◽  
Full Control ◽  
Site Selectivity ◽  
Important Approach ◽  
Distinct Character ◽  
Ruthenium Catalysis ◽  
Material Sciences ◽  
Site Selective

Synthetic transformations of otherwise inert C–H bonds have emerged as a powerful tool for molecular modifications during the last decades, with broad applications towards pharmaceuticals, material sciences and crop protection. Consistently, a key challenge in C–H activation chemistry is the full control of site-selectivity. In addition to substrate control through steric hindrance or kinetic acidity of C–H bonds, one important approach for the site-selective C–H transformation of arenes is the use of chelation-assistance through directing groups, therefore leading to proximity-induced ortho-C–H metalation. In contrast, more challenging remote C–H activations at the meta- or para-positions continue to be scarce. Within this review, we demonstrate the distinct character of ruthenium catalysis for remote C–H activations until March 2021, highlighting among others late-stage modifications of bio-relevant molecules. Moreover, we highlight important mechanistic insights by experiments and computation, highlighting the key importance of carboxylate-assisted C–H activation with ruthenium(II) complexes.

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