scholarly journals Docking of Polyethylenimines Derivatives on Cube Rhombellane Functionalized Homeomorphs

Symmetry ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 1048 ◽  
Author(s):  
Beata Szefler ◽  
Przemysław Czeleń
Keyword(s):  
Hydrogen Bonds ◽  
Binding Constants ◽  
Drug Carriers ◽  
Fullerene C60 ◽  
Reference Structure ◽  
Binding Affinities ◽  
Important Goal ◽  
Polymeric Networks ◽  
The World ◽  
Fullerene Complexes

Nowadays, in the world of science, an important goal is to create new nanostructures that may act as potential drug carriers. Among different, real or hypothetical, polymeric networks, rhombellanes are very promising and, therefore, attempts were made to deposit polyethylenimines as possible nano-drug complexes on the cube rhombellane homeomorphs surface. For the search of ligand–fullerene interactions, was used AutoDockVina software. As a reference structure, the fullerene C60 was used. After the docking procedure, the ligands–fullerenes interactions were tested. The important factor determining the mutual affinity of the tested ligands and nanocarriers is the symmetry of the analyzed nanostructures. Here, this feature has the influence on the distribution of such groups like donors and acceptors of hydrogen bonds on the surface of nanoparticles. We calculated the best binding affinities of ligands, values of binding constants and differences relative to C60 molecules. The best binding efficiency was found for linear ligands. It was also found that the shorter the molecule, the better the binding performance, the more the particle grows and the lower the yield. Small structures of ligands react easily with small structures of nanoparticles. The highest positive percentage deviations were obtained for ligand–fullerene complexes showing the highest binding energy values. Detailed analysis of structural properties after docking showed that the values of affinity of the studied indolizine ligands to the rhombellanes surface are correlated with the strength/length of hydrogen bonds formed between them.

scholarly journals Docking of Platinum Compounds on Cube Rhombellane Functionalized Homeomorphs

Symmetry ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 749
Author(s):  
Beata Szefler ◽  
Przemysław Czeleń
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Binding Affinity ◽  
Fullerene C60 ◽  
C60 Fullerene ◽  
Binding Affinities ◽  
Hydrogen Bond Network ◽  
Platinum Compounds ◽  
Anti Cancer ◽  
Bond Network

Platinum compounds are anti-cancer drugs and can bind to canonical purine bases, mainly guanine, found within double helical DNA. Platinum compounds can be transferred directly to pathologically altered sites in a specific and site-oriented manner by nanocarriers as potential nanocarriers for carboplatin. Two types of nanostructures were used as potential nanocarriers for carboplatin, the first were functionalized C60 fullerene molecules and the second were rhombellanes. The analyzed nanostructures show considerable symmetry, which affects the affinity of the studied nanocarriers and ligands. Thus symmetry of nanostructures affects the distribution of binding groups on their surface. After the docking procedure, analysis of structural properties revealed many interesting features. In all described cases, binding affinities of complexes of platinum compounds with functionalized fullerene C60 are higher compared with affinities of complexes of platinum compounds with rhombellane structures. All platinum compounds easily create complexes with functionalized fullerene C60, CID_16156307, and at the same time show the highest binding affinity. The binding affinities of lobaplatin and heptaplatin are higher compared with oxaliplatin and nedaplatin. The high value of binding affinity and equilibrium constant K is correlated with creation of strong and medium hydrogen bonds or is correlated with forming a hydrogen bond network. The performed investigations enabled finding nanocarriers for lobaplatin, heptaplatin, oxaliplatin and nedaplatin molecules.

scholarly journals SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion

2021 ◽  
Author(s):  
Dhiraj Mannar ◽  
James W. Saville ◽  
Xing Zhu ◽  
Shanti S. Srivastava ◽  
Alison M. Berezuk ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Hydrogen Bonds ◽  
Binding Affinity ◽  
Spike Protein ◽  
Strong Interactions ◽  
Binding Affinities ◽  
Salt Bridges ◽  
The World

The newly reported Omicron variant is poised to replace Delta as the most rapidly spread SARS-CoV-2 variant across the world. Cryo-EM structural analysis of the Omicron variant spike protein in complex with human ACE2 reveals new salt bridges and hydrogen bonds formed by mutated residues R493, S496 and R498 in the RBD with ACE2. These interactions appear to compensate for other Omicron mutations such as K417N known to reduce ACE2 binding affinity, explaining our finding of similar biochemical ACE2 binding affinities for Delta and Omicron variants. Neutralization assays show that pseudoviruses displaying the Omicron spike protein exhibit increased antibody evasion, with greater evasion observed in sera obtained from unvaccinated convalescent patients as compared to doubly vaccinated individuals (8- vs 3-fold). The retention of strong interactions at the ACE2 interface and the increase in antibody evasion are molecular factors that likely contribute to the increased transmissibility of the Omicron variant.

scholarly journals Interactions of Indomethacin with Functionalized Rhombellanes – a Molecular Docking Study

2020 ◽  
Vol 92 (4) ◽  
pp. 503-509
Author(s):  
Raluca Pop ◽  
Dušanka Janežič
Keyword(s):  
Drug Carriers ◽  
Docking Study ◽  
Fullerene C60 ◽  
Inflammatory Activity ◽  
Binding Affinities ◽  
Molecular Docking Study ◽  
New Class ◽  
Anti Inflammatory ◽  
Carbon Based Nanomaterials ◽  
Homo Lumo

The specific properties of carbon-based nanomaterials like fullerenes and graphenes have attracted a continuous interest for their possible use as drug carriers. The functionalization of these nanomaterials can lead to the variation or improvement of the required properties, in order to lead to the design of the most suitable compounds within a specific field. In this regard, the possible use of a new class of nanostructures -the rhombellanes- as nanocarriers is investigated. The aim of the paper is to study the interactions of indomethacin and four analogues with anti-inflammatory activity on 13 rhombellanes (three of them with a hyper-adamantane motif, Ada-rbl, three cube-rhombellane homeomorphs, C-rbl, and seven cube-rhombellane-ether/amine structures). Five compounds with anti-inflammatory activity have been docked to the surface of the rhombellanes; comparisons with the results obtained for fullerene C60 have been performed. The best binding affinities for the indomethacin and its derivatives have been obtained for two types of rhombellanes, Ada-rbl and C-rbl. The indomethacin analogue I4 shows an increased binding affinity for C-rbl.420, similar to the value obtained for C60. Best results have been obtained for rhombellane derivatives characterized by smaller HOMO-LUMO gaps.

scholarly journals A Computational and Literature-Based Evaluation for a Combination of Chiral Anti-CoV Drugs to Block and Eliminate SARS-CoV-2 Safely

2021 ◽  
Author(s):  
Mohd. Suhail
Keyword(s):  
Side Effects ◽  
Jc Virus ◽  
Computational Study ◽  
Human Cells ◽  
The Body ◽  
Binding Affinities ◽  
Chiral Drugs ◽  
Main Protease ◽  
The World ◽  
Second Wave

<p><a>It has been a great challenge for scientists to develop an anti-covid drug/vaccine with fewer side effects, since the coronavirus began. Of course, the prescription of chiral drugs (chloroquine or hydroxychloroquine) has been proved wrong because these chiral drugs neither kill the virus nor eliminate it from the body, but block SARS-CoV-2 from binding to human cells. Another hurdle in front of the world, is not only the positive test of the patient recovered from coronavirus but also the second wave of Covid 19. Hence, the word demands such a drug or drug combination which not only prevents the entry of SARS-CoV-2 in the human cell but also eliminates it or its material from the body completely. The presented computational study explains (i) why the prescription of chiral drugs was not satisfactory (ii) what types of modification can make their prescription satisfactory (iii) the mechanism of action of chiral drugs (chloroquine and hydroxychloroquine) to block SARS-CoV-2 from binding to human cells, and (iv) the strength of mefloquine to eliminate SARS-CoV-2. As the main protease (M<b><sup>pro</sup></b>) of microbes is considered as an effective target for drug design and development, the binding affinities of mefloquine with the main proteases (M<sup>pros</sup>) of JC virus and SARS-CoV-2, were calculated, and then compared to know the eliminating strength of mefloquine against SARS-CoV-2. The main protease (M<sup>pro</sup>) of JC virus was taken because mefloquine has already shown a tremendous result of eliminating it from the body. The current study includes the docking results and literature data in support of the prescription of a combination of S-(+)-hydroxychloroquine and (+) mefloquine. Besides, the presented study also confirms that the prescription of only hydroxychloroquine would not be so effective as in combined form with mefloquine.</a></p>

scholarly journals Mergers decision in Japanese small mutual banks: efficiency improvement or empire buildings?

2009 ◽  
Vol 7 (2) ◽  
pp. 117-125 ◽  
Author(s):  
Nobuyoshi Yamori ◽  
Kozo Harimaya
Keyword(s):  
Cost Efficiency ◽  
Stochastic Frontier ◽  
Efficiency Improvement ◽  
Important Goal ◽  
Stochastic Frontier Approach ◽  
Credit Associations ◽  
Bank Managers ◽  
The World ◽  
Mutual Banks ◽  
Credit Association

With the number of bank consolidations increasing around the world since the 1990s, several studies have examined what factors drive banks to consolidate, and some argue that bank managers who have a motive of empire buildings choose mergers. In this study, we deal with mergers among Japanese small mutual banks (credit associations or Shinkin banks) during the period 1996 to 2005. Japanese credit associations have been experiencing an unprecedented wave of consolidation, with their number decreasing from 410 (March 1996) to 292 (April 2006). Interestingly, unlike stock companies, mutual companies are often expected to be weak in terms of disciplining managers. If so, mutual banks tend to choose inefficient mergers at the expense of other stakeholders. Here, we use the stochastic frontier approach (SFA) to obtain “cost efficiency” proxy. We find that while the efficiency of acquiring credit associations decreases during the merger period, mergers do ultimately improve efficiency. Based on our results we find that raising efficiency, not for building empires, is an important goal for such credit association mergers.

scholarly journals Dendrimers as Drug Carriers. A New Approach to Increase the Potential of Bioactive Natural Products

2006 ◽  
Vol 1 (7) ◽  
pp. 1934578X0600100
Author(s):  
Costas Demetzos
Keyword(s):  
Natural Products ◽  
Drug Delivery Systems ◽  
Drug Carriers ◽  
Water Soluble ◽  
World Health ◽  
New Approach ◽  
Bioactive Natural Products ◽  
The World ◽  
Poorly Water Soluble ◽  
Health Organization

Nanotechnology is a challenging field in science and its application in medicine will bring significant advantages in the treatment of diseases. According to the World Health Organization there is a need for improved therapies against cancer, AIDS and Alzheimer's disease. The new therapies include the design of drug delivery systems, which are able to deliver new bioactive natural products to the target tissues. Dendrimers are hyperbranched polymers with well defined structure and molecular weight; they are composed of a central core and repeated branching units; they have a globular shape, low polydispersity and large void internal spaces that can be used for the encapsulation and delivery of many classes of compounds. Nanosystems, such as dendrimers, can achieve successful administration of poorly water-soluble compounds and those with narrow therapeutic indices.

New multidentate ligands. XXI. Synthesis, proton, and metal ion binding affinities of N,N′,N″-tris[2-(N-hydroxycarbamoyl)ethyl]-1,3,5-benzenetricarboxamide (BAMTPH)

1983 ◽  
Vol 61 (12) ◽  
pp. 2740-2744 ◽  
Author(s):  
Isao Yoshida ◽  
Ichiro Murase ◽  
Ramunas J. Motekaitis ◽  
Arthur E. Martell
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Binding Constants ◽  
Cation Binding ◽  
Ion Binding ◽  
Binding Affinities ◽  
Metal Ion Binding ◽  
Trivalent Metal ◽  
Equilibrium Data ◽  
Trivalent Metal Ions

Synthesis of a new tris-bidentate multidentate ligand, N,N′,N″-tris[2-(N-hydroxycarbamoyl)ethyl]-1,3,5-benzenetricarboxamide (BAMTPH), designed for the binding of trivalent metal ions such as Fe(III), Ga(III), and Al(III), is described. Its cation binding affinities for hydrogen ion and for Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Ga(III), and Al(III) ions are described, and the equilibrium data are compared with those of analogous ligands. The binding constants of trivalent metal ions with the ligand do not show a chelate effect relative to the binding to individual bidentate hydroxamic acids.

Exploring halide anion affinities to native cyclodextrins by mass spectrometry and molecular modelling

2017 ◽  
Vol 24 (3) ◽  
pp. 269-278 ◽  
Author(s):  
Chongsheng Xu ◽  
Nan He ◽  
Zhenhua Li ◽  
Yanqiu Chu ◽  
Chuan-Fan Ding
Keyword(s):  
Gas Phase ◽  
Density Functional ◽  
Binding Constants ◽  
Density Functional Theory Calculations ◽  
Collision Induced Dissociation ◽  
Binding Affinities ◽  
Cyclodextrin Complex ◽  
Halide Anion ◽  
Mass Frame ◽  
The Stability

The binding affinities of cyclodextrins complexation with chlorine (Cl−), bromine (Br−) and iodine (I−), were measured by mass spectrometric titrimetry, and the fitting of the binding constants was based on the concentration measurement of the cyclodextrin equilibrium. The binding constants (lg Ka) for α-, β- or γ-cyclodextrin with Cl− were 3.99, 4.03 and 4.11, respectively. The gas-phase binding affinity of halide anions for native cyclodextrins was probed by collision-induced dissociation. In collision-induced dissociation, the centre-of-mass frame energy results revealed that in the gas phase, for the same type of cyclodextrin, the stability of the complexes decreased in order: Cl > Br > I, and for the same halide anion, the binding stability of the complex with α-, β- or γ-cyclodextrin decreased in the order: γ-cyclodextrin >β-cyclodextrin > α-cyclodextrin. The density functional theory calculations showed that halide anion binding on the primary face had a lower energy than the secondary face and hydrogen bonding was the main driving force for complex formation. The higher stability of the γ-cyclodextrin complex with the Cl anion can be attributed to the higher charge density of the Cl anion and better flexibility of γ-cyclodextrin.

Developing Meaning for Algebraic Symbols: Possibilities and Pitfalls

2008 ◽  
Vol 13 (8) ◽  
pp. 478-483
Author(s):  
John K. Lannin ◽  
Brian E. Townsend ◽  
Nathan Armer ◽  
Savanna Green ◽  
Jessica Schneider
Keyword(s):  
High School ◽  
Middle Grades ◽  
Deep Understanding ◽  
College Experiences ◽  
Important Goal ◽  
Symbolic Representations ◽  
Mathematical Symbols ◽  
The World ◽  
Formal Algebra ◽  
College Calculus

An important goal of school mathematics involves helping students use the powerful forms of representation that have been developed over the centuries through the work of mathematicians throughout the world. However, challenges exist in encouraging students to develop meaning for the mathematical symbols used in formal algebra. Research has demonstrated that students often fail to develop a deep understanding of the meaning of symbolic representations of variables (e.g., Booth 1984; Clement 1982), so much so that Thompson (1994) found that a limited understanding of the meaning of variables negatively impacts students who later take college calculus. The question arises as to how we can develop meaning for formal algebraic symbols in the middle grades so that instruction can build on this meaning throughout students' high school and college experiences.

World Englishes in language testing: a call for research

English Today ◽  
2006 ◽  
Vol 22 (4) ◽  
pp. 32-39 ◽  
Author(s):  
Hyun-Ju Kim
Keyword(s):  
World Wide ◽  
Native Speakers ◽  
Native Language ◽  
Language Testing ◽  
Oral Proficiency ◽  
World Englishes ◽  
Global Changes ◽  
Important Goal ◽  
The World ◽  
Native Speakers Of English

Native speakers of English are a minority; there are far more non-native speakers in the world (cf. Kachru 1997, Pennycook 2001). In addition, native speakers' standard or ‘correct’ English, in terms of its grammar and phonology, is not always useful or even appropriate in international contexts (cf. Gisborne 2000, Newbrook 1998, Shim 1999). However, despite global changes in the use of the language, the norms for ENL (English as a Native Language) remain dominant, most notably for the assessment of oral proficiency. Yet it is a major deficiency in the use of international oral tests that the proficiency of non-native speakers is measured against unrealistic and irrelevant standards (cf. Jenkins, 1996). The present paper focuses on the need to revisit the testing of English oral proficiency for non-native speakers, bearing in mind that English is used for world-wide communication and that being able to understand one another (cf. McKay, 2002) is the most important goal.

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