A Study Modeling Bridged Nucleic Acid-Based ASOs and Their Impact on the Structure and Stability of ASO/RNA Duplexes.

Antisense medications treat diseases that cannot be treated using traditional pharmacological technologies. Nucleotide monomers of bare and phosphorothioate (PS)-modified LNA, N-MeO-amino-BNA, 2',4'-BNANC[NH], 2',4'-BNANC[NMe], and N-Me-aminooxy-BNA antisense modifications were considered for a detailed DFT-based quantum chemical study to estimate their molecular-level structural and electronic properties. Oligomer hybrid duplex stability is described by performing an elaborate MD simulation study by incorporating the PS-LNA and PS-BNA antisense modifications onto 14-mer ASO/RNA hybrid gapmer type duplexes targeting protein PTEN mRNA nucleic acid sequence (5'-CTTAGCACTGGCCT-3'/3'-GAAUCGUGACCGGA-5'). Replica sets of MD simulations were performed accounting to two data sets, each set simulated for 1 µs simulation time. Bulk properties of oligomers are regulated by the chemical properties of their monomers. As such, the primary goal of this work focused on establishing an organized connection between the monomeric BNA nucleotide's electronic effects observed in DFT studies and the macroscopic behavior of the BNA antisense oligomers, as observed in MD simulations. The results from this study predicted that spatial orientation of MO-isosurfaces of the BNA nucleotides are concentrated in the nucleobase region. These BNA nucleotides may become less accessible for various electronic interactions when coupled as ASOs forming duplexes with target RNAs and when the ASO/RNA duplexes further bind with the RNase H. Understanding such electronic interactions is crucial to design superior antisense modifications with specific electronic properties. Also, for the particular nucleic acid sequence solvation of the duplexes although were higher compared to the natural oligonucleotides, their binding energies being relatively lower may lead to decreased antisense activity compared to existing analogs such as the LNAs and MOEs. Fine tuning these BNAs to obtain superior binding affinity is thus a necessity.

In Situ Ni(II) Complexation Induced Deprotonation of Bis-Thiourea-Based Tweezers in DMSO-Water Medium: An Approach toward Recognition of Fluoride Ions in Water with Organic Probe Molecules.

Recognition of fluoride in water through the fluoride-induced Brönsted acid-base deprotonation reaction of an organic probe molecule is still a challenging task owing to the lower basicity of fluoride ions and the instability of the conjugate base of the probe molecules in aqueous medium. Herein, we report a complementary strategy in which the conjugate base of the studied bis-thiourea molecule in dimethyl sulfoxide (DMSO) medium is simultaneously stabilized through chelation of the Ni(II) ion, which eventually facilitates the recognition of the fluoride ion in water samples. The recognition methodology is validated colorimetrically and electrochemically, and finally, the applicability of the approach is explored with water samples collected from fluoride-affected areas. The limit of detection value for the fluoride ion in water medium was found to be 0.2 and 0.3 ppm with UV-visible spectroscopy and differential pulse voltammetry measurements, respectively. The methodology is also demonstrated on a paper strip for the detection of the fluoride ion with the naked eye and a smartphone-based RGB sensor. The scheme has been shown to be effective in enhancing the aqueous fluoride recognition ability of the organic probe molecules with acidic hydrogen prone to deprotonation by the fluoride ion.

Reaction Mechanism and Kinetics for the Selective Hydrogenation of Carbon Dioxide to Formic Acid and Methanol over the [Cu2]0,±1 Dimer.

With the rapid growth of industrialization, deforestation, and burning of fossil fuels, undeniably there has been an incredible escalation of the CO2 concentration in the atmosphere. In order to mitigate the problem, the capture and utilization of CO2 in different value-added chemicals have thus remained topics of concerned research for more than a decade. Accordingly, we have performed molecular -level catalytic hydrogenation of CO2 to formic acid using bare [Cu2]0,±1 dimers as catalysts. The entire investigation has been performed using a density functional theory (DFT) method employing the Perdew-Burke-Ernzerhof (PBE) functional with the def2TZVPP basis set to explore the different possible routes and efficiency of the catalysts. Results reveal the feasibility of H2 dissociation on all three Cu2, Cu2+, and Cu2- dimers. The negatively charged hydride formed during H2 dissociation on Cu2 and Cu2+ dimers facilitates the formation of the HCOO* intermediate over COOH*, thereby providing product selectivity for HCOOH above CO. However, the reaction on the Cu2- dimer forms both HCOO* and COOH* intermediates, but HCOO*, being kinetically more favorable, results in HCOOH production. The free-energy change suggests that the complete reaction on Cu2 and Cu2+ dimers forms a stable product compared to the Cu2- dimer. Furthermore, H3COH production is studied using the title catalysts via the obtained HCOOH* intermediate from the reaction channel. Transition state theory (TST) has been considered to evaluate the rate constants for each step of the reaction. Overall results suggest Cu2 to be better compared to Cu2+ and Cu2- dimers for HCOOH formation and Cu2+ over Cu2 and Cu2- dimers to be more efficient for H3COH formation. This work opens the way for further investigation of the reaction mechanism and development of an efficient catalyst for CO2 hydrogenation.

Design of LNA Analogues Using a Combined Density Functional Theory and Molecular Dynamics Approach for RNA Therapeutics.

Antisense therapeutics treat a wide spectrum of diseases, many of which cannot be addressed with the current drug technologies. In the quest to design better antisense oligonucleotide drugs, we propose five novel LNA analogues (A1-A5) for modifying antisense oligonucleotides and establishing each with the five standard nucleic acids: adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U). Monomer nucleotides of these modifications were considered for a detailed Density Functional Theory (DFT)-based quantum chemical analysis to determine their molecular-level structural and electronic properties. A detailed MD simulation study was done on a 14-mer ASO (5'-CTTAGCACTGGCCT-3') containing these modifications targeting PTEN mRNA. Results from both molecular- and oligomer-level analysis clearly depicted LNA-level stability of the modifications, the ASO/RNA duplexes maintaining stable Watson-Crick base pairing preferring RNA-mimicking A-form duplexes. Notably, monomer MO isosurfaces for both purines and pyrimidines were majorly distributed on the nucleobase region in modifications A1 and A2 and in the bridging unit in modifications A3, A4, and A5, suggesting that A3/RNA, A4/RNA, and A5/RNA duplexes interact more with the RNase H and solvent environment. Accordingly, solvation of A3/RNA, A4/RNA, and A5/RNA duplexes was higher compared to that of LNA/RNA, A1/RNA, and A2/RNA duplexes. This study has resulted in a successful archetype for creating advantageous nucleic acid modifications tailored for particular needs, fulfilling a useful purpose of designing novel antisense modifications, which may overcome the drawbacks and improve the pharmacokinetics of existing LNA antisense modifications.

Metal-free S-arylation of 5-mercaptotetrazoles and 2-mercaptopyridine with unsymmetrical diaryliodonium salts.

Herein, we demonstrate the application of unsymmetrical iodonium salts towards S-arylation of heterocyclic thiols (especially tetrazole-5-thiols and pyridine-2-thiol) under metal-free conditions, affording a diverse range of di(hetero)aryl thioethers in moderate to good yields. A detailed study on the effects of counter-anions and the auxiliary of iodonium salts was conducted. Suitable auxiliary selection of the unsymmetrical iodonium salt offers flexibility for a wide range of aryl moieties and its incorporation into S-arylation. The DFT study supports the experimental observations of chemoselective arylation.