Synthesis and properties of novel 2′-C,4′-C-ethyleneoxy-bridged 2′-deoxyribonucleic acids with exocyclic methylene groups

2016 ◽  
Vol 14 (40) ◽  
pp. 9481-9484 ◽  
Author(s):  
Takashi Osawa ◽  
Satoshi Obika ◽  
Yoshiyuki Hari
Keyword(s):  
Binding Affinity ◽  
Modified Oligonucleotides ◽  
Strong Binding ◽  
Nuclease Resistance ◽  
Methylene Groups ◽  
Exocyclic Methylene

Three methylene-EoDNAs were synthesized from 5-methyluridine and their modified oligonucleotides showed strong binding affinity with ssRNA and high nuclease resistance.

scholarly journals Synthesis and Antisense Properties of 2′β-F-Arabinouridine Modified Oligonucleotides with 4′-C-OMe Substituent

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2374 ◽  
Author(s):  
Xiao-Yang He ◽  
Jing Wang ◽  
Dan-Dan Lu ◽  
Sheng-Qi Wang
Keyword(s):  
Chemical Modification ◽  
Binding Affinity ◽  
Therapeutic Strategy ◽  
Modified Oligonucleotides ◽  
Nuclease Resistance ◽  
Modified Oligonucleotide

A novel 2′-F,4′-C-OMe–arabinouridine (araU) was successfully synthesized and introduced into oligonucleotides. The oligonucleotide containing 2′-F,4′-C-OMe–araU exhibited improved nuclease resistance and RNA hybridizing selective ability relative to 2′-F–araU. In particular, when 2′-F,4′-C-OMe–araU inserted into C–H⋯F–C bonding-favorable 5′–uridine–purine–3′ steps, the modified oligonucleotide showed remarkable binding affinity and selectivity to RNA complements. Thus, 2′-F,4′-C-OMe–araU has valuable antisense properties and can be used as novel chemical modification for antisense therapeutic strategy.

scholarly journals Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics

2021 ◽  
Author(s):  
Tomio Iwasaki ◽  
Masashi Maruyama ◽  
Tatsuya Niwa ◽  
Toshiki Sawada ◽  
Takeshi Serizawa
Keyword(s):  
Methyl Methacrylate ◽  
Binding Affinity ◽  
Molecular Simulation ◽  
Dynamics Simulation ◽  
Binding Affinities ◽  
Materials Informatics ◽  
Poly Methyl Methacrylate ◽  
Strong Binding ◽  
Experimental Values ◽  
Pmma Resin

AbstractPeptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on molecular dynamics simulation for the purpose of covering the resin surface with adhesive peptides, which were expected to result in eco-friendly and biocompatible biomaterials. From the results of binding affinity obtained with this molecular simulation, it was confirmed that experimental values could be predicted with errors <10%. By analyzing the simulation data with the response-surface method, we found that three peptides (RWWRPWW, EWWRPWR, and RWWRPWR), which consist of arginine (R), tryptophan (W), and proline (P), have strong binding affinity to the PMMA resin. These amino acids were effective because arginine and tryptophan have strong binding affinities for methoxycarbonyl groups and methyl groups, which are the main constituents of the PMMA resin, and proline stabilizes the flat zigzag structures of the peptides in water. The strong binding affinities of the three peptides were confirmed by experiments (surface plasmon resonance methods).

scholarly journals Epitope-Based Peptide Vaccine Against Fructose-Bisphosphate Aldolase of Madurella mycetomatis Using Immunoinformatics Approaches

2018 ◽  
Vol 12 ◽  
pp. 117793221880970 ◽  
Author(s):  
Arwa A Mohammed ◽  
Ayman MH ALnaby ◽  
Solima M Sabeel ◽  
Fagr M AbdElmarouf ◽  
Amina I Dirar ◽  
...  
Keyword(s):  
B Cell ◽  
Binding Affinity ◽  
Mhc Class Ii ◽  
Bacterial Infections ◽  
Peptide Vaccine ◽  
Fructose Bisphosphate ◽  
Mhc I ◽  
Strong Binding ◽  
Fructose Bisphosphate Aldolase ◽  
Madurella Mycetomatis

Background: Mycetoma is a distinct body tissue destructive and neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections ( actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi ( eumycetoma) such as Madurella mycetomatis. To date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma. Aim: The aim of this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches. Methods and materials: Fructose-bisphosphate aldolase of M. mycetomatis sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in Immune Epitope Database for B-cell, T-cell MHC class II and class I. Then the proposed peptides were docked using Autodock 4.0 software program. Results and conclusions: The proposed and promising peptides KYLQ show a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC I alleles and FFKEHGVPL that shows a very strong binding affinity to MHC II and MHC I alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against fructose-bisphosphate aldolase of M. mycetomatis. This study recommends an in vivo assessment for the most promising peptides especially FFKEHGVPL.

scholarly journals Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases

2021 ◽  
Vol 17 ◽  
pp. 622-629
Author(s):  
Naohiro Horie ◽  
Takao Yamaguchi ◽  
Shinji Kumagai ◽  
Satoshi Obika
Keyword(s):  
Nucleic Acid ◽  
Binding Affinity ◽  
Antisense Oligonucleotides ◽  
Modified Oligonucleotides ◽  
Biophysical Properties ◽  
Chemical Modifications ◽  
Antisense Technology ◽  
Strong Affinity ◽  
The Stability

Chemical modifications have been extensively used for therapeutic oligonucleotides because they strongly enhance the stability against nucleases, binding affinity to the targets, and efficacy. We previously reported that oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing the thymine (T) nucleobase show excellent biophysical properties for applications in antisense technology. In this paper, we describe the synthesis of GuNA[Me] phosphoramidites bearing other typical nucleobases including adenine (A), guanine (G), and 5-methylcytosine (mC). The phosphoramidites were successfully incorporated into oligonucleotides following the method previously developed for the GuNA[Me]-T-modified oligonucleotides. The binding affinity of the oligonucleotides modified with GuNA[Me]-A, -G, or -mC toward the complementary single-stranded DNAs or RNAs was systematically evaluated. All of the GuNA[Me]-modified oligonucleotides were found to have a strong affinity for RNAs. These data indicate that GuNA[Me] could be a useful modification for therapeutic antisense oligonucleotides.

Supramolecular self-assemblies of inverted cucurbit[7]uril with biogenic amines

2019 ◽  
Vol 43 (1) ◽  
pp. 407-412
Author(s):  
Pei-Hui Shan ◽  
Zhi-Rui Zhang ◽  
Dong Bai ◽  
Bing Bian ◽  
Zhu Tao ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Binding Affinity ◽  
Biogenic Amine ◽  
Binding Sites ◽  
Experimental Results ◽  
Binding Interactions ◽  
Strong Binding

The binding interactions between six biogenic amine guests and the iQ[7] host were investigated. The experimental results have revealed that iQ[7] shows strong binding affinity towards five of the studied biogenic amines, but not histamine, and that the binding sites are different depending on the structure of the biogenic amine.

The remarkable activity and stability of a dye-sensitized single molecular layer MoS2ensemble for photocatalytic hydrogen production

2015 ◽  
Vol 51 (70) ◽  
pp. 13496-13499 ◽  
Author(s):  
Tiantian Jia ◽  
Molly M. J. Li ◽  
Lin Ye ◽  
Sam Wiseman ◽  
Guoliang Liu ◽  
...  
Keyword(s):  
Hydrogen Production ◽  
Binding Affinity ◽  
Molecular Layer ◽  
Single Layer ◽  
Eosin Y ◽  
Photocatalytic Hydrogen Production ◽  
Dye Sensitized ◽  
Strong Binding ◽  
Single Molecular Layer ◽  
Dye Molecule

Single layer MoS2synthesized by exfoliation with Li is demonstrated to take up the dye molecule, Eosin Y, with strong binding affinityviasulfur vacancies.

Abstract 5790: TG-1601 is a novel BET inhibitor with strong binding affinity and long-lasting effect in pre-clinical models

2018 ◽  
Author(s):  
Emmanuel Normant ◽  
Leonid Gorelik ◽  
Rama Shmeis ◽  
Henry Le ◽  
Robert Nisch ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Bet Inhibitor ◽  
Lasting Effect ◽  
Strong Binding ◽  
Clinical Models

scholarly journals A 2,3-dialkoxynaphthalene-based naphthocage

2020 ◽  
Vol 56 (6) ◽  
pp. 888-891 ◽  
Author(s):  
Song-Bo Lu ◽  
Hongxin Chai ◽  
Jas S. Ward ◽  
Mao Quan ◽  
Jin Zhang ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Organic Cations ◽  
Strong Binding

A 2,3-dialkoxynaphthalene-based naphthocage was synthesized. It shows similarly strong binding affinity to organic cations as the 2,6-dialkoxynaphthalene-based naphthocage but different guest preference and conformational response.

Hydrogen Uptake on Coordinatively Unsaturated Metal Sites in VSB-5: Strong Binding Affinity Leading to High-Temperature D2/H2 Selectivity

Langmuir ◽  
2017 ◽  
Vol 33 (51) ◽  
pp. 14586-14591 ◽  
Author(s):  
Amit Sharma ◽  
Keith V. Lawler ◽  
Jarod J. Wolffis ◽  
Christopher T. Eckdahl ◽  
Cooper S. McDonald ◽  
...  
Keyword(s):  
High Temperature ◽  
Binding Affinity ◽  
Hydrogen Uptake ◽  
Strong Binding ◽  
Unsaturated Metal Sites ◽  
H2 Selectivity

Interproton allylic spin-spin coupling involving exocyclic groups

1972 ◽  
Vol 25 (8) ◽  
pp. 1669 ◽  
Author(s):  
GP Newsoroff ◽  
S Sternhell
Keyword(s):  
Coupling Constants ◽  
Spin Coupling ◽  
Dihedral Angles ◽  
Ring Size ◽  
Methylene Groups ◽  
Exocyclic Methylene ◽  
Geminal Coupling ◽  
The Absolute ◽  
Absolute Magnitudes ◽  
Spin Spin Coupling

N.m.r. parameters for 55 compounds incorporating exocyclic groups were obtained. In unstrained structures the relative (as well as the absolute) magnitudes of transoid and cisoid allylic coupling constants depend on the magnitudes of the dihedral angles but additional effects were also identified. The magnitudes of geminal coupling constants between the protons of exocyclic methylene groups and of homoallylic coupling constants involving exocyclic ethylidene and isopropylidene groups vary systematically with ring size.

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