Carbon and boron nanotubes as a template material for adsorption of 6-Thioguanine chemotherapeutic: a molecular dynamics and density functional approach.

Abstract:

:The interaction of 6-Thioguanine molecule, an antitumor drug with carbon nanotube and boron nitride nanotube (BNNT) is investigated using molecular dynamics simulations. Based on the obtained results, the strongest negative van der Waals interaction is found between 6-TG and BNNT among the studied nanotubes, which indicated BNNT is a better nanocarrier of the 6-TG drug than CNT within biological systems. Moreover, the adsorption and electronic properties of the 6-Thioguanine interacted with boron-nitride nanotube has been studied within the framework of density functional theory calculations. The negative binding energy values denote that there is the favorable interaction between 6-TG drug and BNNT at the studied 6-TG/BNNT complexes. Also, the amounts of the binding energies indicated that the 6-Thioguanine molecule physically interacts with the surface of BNNT. The values of electron densities and their Laplacian have been analyzed using the Bader's theory of atoms in molecules to characterize the nature of the intermolecular interactions through the topological parameters. We hope that the results of this work may provide useful information about the nature of the nanotube-drug molecule interactions and highlight the ability of these materials to be used as an adsorbent enhancing delivery of drug to cancer cells. Communicated by Ramaswamy H. Sarma.

journal_name

J Biomol Struct Dyn

authors

Hasanzade Z,Raissi H

doi

10.1080/07391102.2019.1585951

subject

Has Abstract

pub_date

2020-02-01 00:00:00

pages

697-707

issue

3

eissn

0739-1102

issn

1538-0254

journal_volume

38

pub_type

杂志文章
  • The effect of the amino-acid side chains on the energy profiles for ion transport in the gramicidin A channel.

    abstract::Computations on the energy profiles for Na+ in the gramicidin A (GA) channel have been extended by introducing the effect, previously neglected, of the amino acid side chains of GA, fixed in their most stable conformations. The calculations have been performed in two approximations: 1) with the ethanolamine tail fixed...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1985.10507605

    authors: Etchebest C,Pullman A

    更新日期:1985-02-01 00:00:00

  • Effects of low urea concentrations on protein-water interactions.

    abstract::Solvent properties of aqueous media (dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were measured in the coexisting phases of Dextran-PEG aqueous two-phase systems (ATPSs) containing .5 and 2.0 M urea. The differences between the electrostatic and hydrophobic properties of...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1135823

    authors: Ferreira LA,Povarova OI,Stepanenko OV,Sulatskaya AI,Madeira PP,Kuznetsova IM,Turoverov KK,Uversky VN,Zaslavsky BY

    更新日期:2017-01-01 00:00:00

  • Transmembrane helix 6 observed at the interface of β2AR homodimers in blind docking studies.

    abstract::Peptide- and protein-protein dockings were carried out on β2-adrenergic receptor (β2AR) to confirm the presence of transmembrane helix 6 (TM6) at the interface region between two β2AR monomers, thereby its possible role in dimerization as suggested in numerous experimental and computational studies. Initially, a porti...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2014.962094

    authors: Koroglu A,Akten ED

    更新日期:2015-01-01 00:00:00

  • Refined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents.

    abstract::Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1688196

    authors: Pan Z,Wang Y,Gu X,Wang J,Cheng M

    更新日期:2020-10-01 00:00:00

  • Effect of base stacking on the relative thermodynamic stability of oligonucleotide complexes: a spectroscopic study.

    abstract::Three-strand oligonucleotide complexes are employed to assess the effect of base stacking and base pair mismatch on the relative thermodynamic stabilities of oligonucleotide duplexes. The melting behavior of three-strand oligonucleotide complexes incorporating nicks and gaps as well as internal single base mismatches ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2004.10506995

    authors: Murphy D,Doyle H,Eritja R,Redmond G

    更新日期:2004-10-01 00:00:00

  • What is paradoxical about Levinthal paradox?

    abstract::We would be tempted to state that there has never been a Levinthal paradox. Indeed, Levinthal raised an interesting problem about protein folding, as he realized that proteins have no time to explore exhaustively their conformational space on the way to their native structure. He did not seem to find this paradoxical ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2002.10506850

    authors: Rooman M,Dehouck Y,Kwasigroch JM,Biot C,Gilis D

    更新日期:2002-12-01 00:00:00

  • Nonionic but water soluble, [Glycine-Pd-Alanine] and [Glycine-Pd-Valine] complexes. Their synthesis, characterization, antitumor activities and rich DNA/HSA interaction studies.

    abstract::Two novel, neutral and water soluble Pd(II) complexes of formula [Pd(Gly)(Ala)] (1) and [Pd(Gly)(Val)] (2) (Gly, Ala, and Val are anionic forms of glycine, alanine, and valine amino acids, respectively) have been synthesized and characterized by FT-IR, UV-Vis, 1H-NMR, elemental analysis, and molar conductivity measure...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1520647

    authors: Mansouri-Torshizi H,Zareian-Jahromi S,Abdi K,Saeidifar M

    更新日期:2019-08-01 00:00:00

  • Computer-aided drug design of novel PLA2 inhibitor candidates for treatment of snakebite.

    abstract::Phospholipases A(2) (PLA(2)) are enzymes commonly found in snake venoms from Viperidae and Elaphidae families, which are major components thereof. Many plants are used in traditional medicine as active agents against various effects induced by snakebite. This article presents the PLA(2) BthTX-I structure prediction ba...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2009.10507293

    authors: Hage-Melim LI,da Silva CH,Semighini EP,Taft CA,Sampaio SV

    更新日期:2009-08-01 00:00:00

  • Comparison of the structures of the metal-thiolate binding site in Zn(II)-, Cd(II)-, and Hg(II)-metallothioneins using molecular modeling techniques.

    abstract::The first fully energy-minimized structures for a series of structurally related metal complexes of the important mammalian metal binding protein metallothionein are described. The structures were calculated based on structural information obtained from existing spectroscopic and crystallographic data, and minimized u...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1997.10508139

    authors: Fowle DA,Stillman MJ

    更新日期:1997-02-01 00:00:00

  • An efficient automated computer vision based technique for detection of three dimensional structural motifs in proteins.

    abstract::As the number of available three dimensional coordinates of proteins increases, it is now recognized that proteins from different families and topologies are constructed from independent motifs. Detection of specific structural motifs within proteins aids in understanding their role and the mechanism of their operatio...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1992.10507955

    authors: Fischer D,Bachar O,Nussinov R,Wolfson H

    更新日期:1992-02-01 00:00:00

  • Mining for novel tumor suppressor genes using a shortest path approach.

    abstract::Cancer, being among the most serious diseases, causes many deaths every year. Many investigators have devoted themselves to designing effective treatments for this disease. Cancer always involves abnormal cell growth with the potential to invade or spread to other parts of the body. In contrast, tumor suppressor genes...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1042915

    authors: Chen L,Yang J,Huang T,Kong X,Lu L,Cai YD

    更新日期:2016-01-01 00:00:00

  • Investigation of domain motions in bacteriophage T4 lysozyme.

    abstract::Hinge-bending in T4 lysozyme has been inferred from single amino acid mutant crystalline allomorphs by Matthews and coworkers. This raises an important question: are the different conformers in the unit cell artifacts of crystal packing forces, or do they represent different solution state structures? The objective of...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1994.10508751

    authors: Arnold GE,Manchester JI,Townsend BD,Ornstein RL

    更新日期:1994-10-01 00:00:00

  • Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19.

    abstract::Medicinal herbs have proved along history to be a source of multiple cures. In this paper, we demonstrate how hydroxychloroquine can act as a good inhibitor of SARS-CoV-2 Spike protein receptor-binding-domain using molecular docking studies. We also unveil how hydroxychloroquine can interfere in the prevention of Lys3...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1796809

    authors: Sehailia M,Chemat S

    更新日期:2020-07-22 00:00:00

  • Searching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets.

    abstract::The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worl...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1869096

    authors: Almeida JSFD,Botelho FD,de Souza FR,Dos Santos MC,Goncalves ADS,Rodrigues RLB,Cardozo M,Kitagawa DAS,Vieira LA,Silva RSF,Cavalcante SFA,Bastos LDC,Nogueira MOT,de Santana PIR,Brum JOC,Nepovimova E,Kuca K,LaPlante SR,G

    更新日期:2021-01-08 00:00:00

  • Glycation, oxidation and glycoxidation of IgG: a biophysical, biochemical, immunological and hematological study.

    abstract::Glycation and oxidation induce structural alterations in the proteins in an interdependent manner with consequent pathological implications. The published literature presents wide range of modifications in conformational characteristics of proteins by glycation and oxidation; however, there is little data that could e...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2017.1365770

    authors: Islam S,Moinuddin,Mir AR,Raghav A,Habib S,Alam K,Ali A

    更新日期:2018-08-01 00:00:00

  • Diffusion-collision model for the folding kinetics of the lambda-repressor operator-binding domain.

    abstract::The operator-binding domain of the lambda-repressor contains five alpha-helices and an extended N-terminal arm in the crystal structure determined by Pabo and Lewis reported in Nature 298, 443, 1982 (1). The four helices form a "box" enclosing a hydrophobic core with the fifth helix interacting with the equivalent hel...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1984.10507515

    authors: Bashford D,Weaver DL,Karplus M

    更新日期:1984-03-01 00:00:00

  • Deciphering the interaction of puerarin with cancer macromolecules: An in silico investigation.

    abstract::The worldwide expanding increment in cancer pervasiveness is disturbing and this disease ranks among the main causes of mortality in both developing and developed countries. Unfortunately, available treatment options come with serious side effects and do not guarantee complete success. Although numerous models have be...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1819425

    authors: Ojo OA,Aruleba RT,Adekiya TA,Sibuyi NRS,Ojo AB,Ajiboye BO,Oyinloye BE,Adeola HA,Fadaka AO

    更新日期:2020-09-14 00:00:00

  • Computational analysis identifies druggable mutations in human rBAT mediated Cystinuria.

    abstract::Culex quinquefasciatus Cqm1 protein acts as the receptor for Lysinibacillus sphaericus mosquito-larvicidal binary (BinAB) toxin that is used worldwide for mosquito control. We found amino acid transporter protein, rBAT, as phylogenetically closest Cqm1 homolog in humans. The present study reveals large evolutionary di...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1784792

    authors: Pandey B,Aarthy M,Sharma M,Singh SK,Kumar V

    更新日期:2020-06-30 00:00:00

  • Exploring the interaction between tyrphostin 9 and human serum albumin using biophysical and computational methods.

    abstract::Tyrphostin 9 (Tyr 9) is a potent platelet-derived growth factor receptor (PDGFR) inhibitor, which induces apoptosis in various cancer cell types. The binding of Tyr 9 to the major transport protein, human serum albumin (HSA) was investigated using several spectroscopic techniques and molecular docking method. Fluoresc...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1673210

    authors: Kandandapani S,Ridzwan NFW,Mohamad SB,Tayyab S

    更新日期:2020-09-01 00:00:00

  • DNA Structure and Polymerase Fidelity: A New Role for A-DNA.

    abstract::Abstract Although the recent structural studies on polymerases have brought new insights on polymerase fidelity, the role of DNA sequence and structure is not well understood. Here, the analysis of the crystal structures of hotspots for polymerase slippage shows that, in the B- form, these sequences share common str...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2000.10506617

    authors: Timsit Y

    更新日期:2000-01-01 00:00:00

  • A potent drug candidature of Cu(II) pyrazino[2,3-f][1,10]phenanthroline complexes with bioactive ligands: synthesis, crystal structures, biomolecular interactions, radical scavenging and cytotoxicities.

    abstract::A novel ternary copper(II) complexes, - [Cu(py-phen)(asn)(NO3)(H2O)] (1) and [Cu(py-phen)(trp)(H2O)]NO3 (2)- (py-phen: pyrazino[2,3-f][1,10]phenanthroline, asn: asparagine, trp: tryptophan), have been synthesized and characterized by CHN analysis, ESI-MS, FTIR and single-crystal X-ray diffraction techniques. Interacti...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2020.1808070

    authors: İnci D,Aydın R,Vatan Ö,Zorlu Y

    更新日期:2020-08-18 00:00:00

  • Hydrolases: the correlation between informational structure and the catalytic sites organization.

    abstract::The novel method allowing identification of protein structure elements responsible for catalytic activity manifestation is proposed. Structural organization of various hydrolases was studied using the ANIS (ANalysis of Informational Structure) method. ANIS allows to reveal a hierarchy of the ELements of Information St...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2008.10507202

    authors: Nekrasov AN,Zinchenko AA

    更新日期:2008-04-01 00:00:00

  • SARS-CoV-2 mutations and where to find them: an in silico perspective of structural changes and antigenicity of the spike protein.

    abstract::Communicated by Ramaswamy H. Sarma. ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 信件

    doi:10.1080/07391102.2020.1844052

    authors: Gonçalves RL,Leite TCR,Dias BP,Caetano CCDS,de Souza ACG,Batista UDS,Barbosa CC,Reyes-Sandoval A,Coelho LFL,Silva BM

    更新日期:2020-11-06 00:00:00

  • Structural analysis of human lysozyme using molecular dynamics simulations.

    abstract::In this study, various molecular dynamics simulations were conducted to investigate the effects of ethanol and temperature on the conformational changes of human lysozyme, which may lead insights into amyloidosis. The analyses of some important structural characteristics, such as backbone root-mean-square deviation, s...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2006.10507115

    authors: Liu HL,Wu YC,Zhao JH,Fang HW,Ho Y

    更新日期:2006-12-01 00:00:00

  • Computational analysis of the thermal stability in thioredoxins: a molecular dynamics approach.

    abstract::The knowledge of the relationship between the three-dimensional structure of a protein and its biological and stability is one of the most challenging problem in protein chemistry, since offers the possibility of changing both the specific action of a protein and its stability. In this work, we have approached the pro...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1998.10508259

    authors: Pedone EM,Bartolucci S,Rossi M,Saviano M

    更新日期:1998-10-01 00:00:00

  • Insights on the structural perturbations in human MTHFR Ala222Val mutant by protein modeling and molecular dynamics.

    abstract::Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural t...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2015.1057866

    authors: Abhinand PA,Shaikh F,Bhakat S,Radadiya A,Bhaskar LV,Shah A,Ragunath PK

    更新日期:2016-01-01 00:00:00

  • Structure-based drug target prioritisation and rational drug design for targeting Chlamydia trachomatis eye infections.

    abstract::Chlamydia trachomatis (C.t) is a major causative of infectious blindness in world. It is a real challenge to combat Chlamydial infection as it is an intracellular pathogen. Hence, it is essential to determine the most potential targets of C.t in order to inhibit or suppress its virulence during its infectious phase. T...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2019.1652691

    authors: Sadhasivam A,Nagarajan H,Umashankar V

    更新日期:2020-07-01 00:00:00

  • Fluorescence studies on the coat protein of alfalfa mosaic virus.

    abstract::The intrinsic luminescence of different forms of the alfalfa mosaic virus (AMV) strain 425 coat protein has been studied, both statically and time resolved. It was found that the emission of the protein (Mr 24,250), which contains two tryptophans at positions 54 and 190 and four tyrosines, is completely dominated by t...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.1986.10508464

    authors: Kan JH,Wijnaendts van Resandt RW,Dekkers HP

    更新日期:1986-02-01 00:00:00

  • Identification of some novel pyrazolo[1,5-a]pyrimidine derivatives as InhA inhibitors through pharmacophore-based virtual screening and molecular docking.

    abstract::The InhA inhibitors play key role in mycolic acid synthesis by preventing the fatty acid biosynthesis pathway. In this present article, Pharmacophore modelling and molecular docking study followed by in silico virtual screening could be considered as effective strategy to identify newer enoyl-ACP reductase inhibitors....

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2018.1465852

    authors: Modi P,Patel S,Chhabria MT

    更新日期:2019-04-01 00:00:00

  • Local structural properties of the V3 loop of Thailand HIV-1 isolate.

    abstract::The model of locally accurate conformation for the HIV-Thailand principal neutralizing determinant (PND) located within the V3 loop of the virus envelope protein gp120 was built in terms of NMR spectroscopy data. To this end, the NMR-based conformational analysis of synthetic molecule representing the peptide copy of ...

    journal_title:Journal of biomolecular structure & dynamics

    pub_type: 杂志文章

    doi:10.1080/07391102.2002.10506801

    authors: Andrianov AM

    更新日期:2002-06-01 00:00:00