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.

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.

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

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

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 Epitope - based peptide vaccine againstFructose-bisphosphate aldolase (FBA)ofMadurella mycetomatisusing immunoinformatics approaches

2018 ◽  
Author(s):  
Arwa A. Mohammed ◽  
Ayman M. H. 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 ◽  
Strong Binding ◽  
Fructose Bisphosphate Aldolase ◽  
Madurella Mycetomatis

AbstractBackgroundMycetoma is a distinct flesh eating and destructive 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. Until 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.The aimof this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches.Methods and MaterialsFructose-bisphosphate aldolase ofMadurella mycetomatisSequence 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 & I. Then the proposed peptides were docked using Autodock 4.0 software program.Results and ConclusionsThe proposed and promising peptides KYLQ shows a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC1 alleles and FFKEHGVPL that show a very strong binding affinity to MHC11and MHC1 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 Madurella mycetomatis. This study recommends an in-vivo assessment for the most promising peptides especially FFKEHGVPL.

scholarly journals In-Silico Study of Some Natural Plant Phyto-compounds for the Identification of Novel Potent Cholinesterase Inhibitors Against Alzheimer Disease

2021 ◽  
Author(s):  
Dhiraj Kumar ◽  
Sanjana Bhagat
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Docking Study ◽  
Inhibitory Effect ◽  
Ache Inhibitor ◽  
Site Analysis ◽  
Strong Binding ◽  
In Silico Studies ◽  
Potent Inhibitory Effect ◽  
Autodock 4.0

The main aim of this study is to identify inhibitory binding potent of the available commercially alkaloids, against the crystal structure of acetylcholinesterase (AChE) protein by in silico studies. The inhibitory data of the compounds should be compared with the internal ligand as well as standard AChE inhibitor Aricept (which is used for the treatment of all stages of Alzheimer&rsquo;s disease). AutoDock 4.0 is used for the docking study, conformational orientation site analysis, and, with the help of docking, we have calculated parameters like binding energy and inhibition constant. Docking's study showed that Glabridin, Isorosmanol, Quercetin, Honokiol, Eckol, Sargaquinoic acid, and Ginsedosides revealed strong binding affinity with the enzyme. Moreover, The ADMET profiling and physicochemical properties of the selected compounds are evaluated using the Molinspiration and Data warrior software. By showing a strong binding affinity value, positive bioactivity score, and good pharmacokinetic properties, the top compound was determined. After evaluation with all parameters, the compound Glabridin and Ginsedosides show the most potent inhibitory effect towards the acetylcholinesterase, so this compound could be used as a novel is required to treat Alzheimer's disease.

scholarly journals Marine derivatives prevent w MUS81 in silico studies

2021 ◽  
Vol 8 (9) ◽  
pp. 210974
Author(s):  
Son Tung Ngo ◽  
Khanh B. Vu ◽  
Minh Quan Pham ◽  
Nguyen Minh Tam ◽  
Phuong-Thao Tran
Keyword(s):  
Binding Affinity ◽  
Binding Free Energy ◽  
Dominant Factor ◽  
Cancer Drug ◽  
Perturbation Approach ◽  
Strong Binding ◽  
In Silico Studies ◽  
Marine Compounds ◽  
Aspergiolide A ◽  
Dynamics Simulations

The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 ( w MUS81) is a potential cancer drug target. In this context, marine fungi compounds were indicated to be able to prevent w MUS81 structure via atomistic simulations. Eight compounds such as D197 ( Tryptoquivaline U ), D220 ( Epiremisporine B ), D67 ( Aspergiolide A ), D153 ( Preussomerin G ), D547 ( 12,13-dihydroxyfumitremorgin C ), D152 ( Preussomerin K ), D20 ( Marinopyrrole B ) and D559 ( Fumuquinazoline K ) were indicated that they are able to prevent the conformation of w MUS81 via forming a strong binding affinity to the enzyme via perturbation approach. The electrostatic interaction is the dominant factor in the binding process of ligands to w MUS81. The residues Trp55, Arg59, Leu62, His63 and Arg69 were found to frequently form non-bonded contacts and hydrogen bonds to inhibitors. Moreover, the influence of the ligand D197 , which formed the lowest binding free energy to w MUS81, on the structural change of enzyme was investigated using replica exchange molecular dynamics simulations. The obtained results indicated that D197 , which forms a strong binding affinity, can modify the structure of w MUS81. Overall, the marine compounds probably inhibit w MUS81 due to forming a strong binding affinity to the enzyme as well as altering the enzymic conformation.

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