当前位置： SCI文献检索 > COMPUTATIONAL BIOLOGY AND CHEMISTRY期刊下所有文献 > Aconitum and Delphinium sp. alkaloids as antagonist modulators of voltage-gated Na+ channels. AM1/DFT electronic structure investigations and QSAR studies.

Aconitum and Delphinium sp. alkaloids as antagonist modulators of voltage-gated Na+ channels. AM1/DFT electronic structure investigations and QSAR studies.

Abstract：

:Early pharmacological studies of Aconitum and Delphinium sp. alkaloids suggested that these neurotoxins act at site 2 of voltage-gated Na(+) channel and allosterically modulate its function. Understanding structural requirements for these compounds to exhibit binding activity at voltage-gated Na(+) channel has been important in various fields. This paper reports quantum-chemical studies and quantitative structure-activity relationships (QSARs) based on a total of 65 natural alkaloids from two plant species, which includes both blockers and openers of sodium ion channel. A series of 18 antagonist alkaloids (9 blockers and 9 openers) have been studied using AM1 and DFT computational methods in order to reveal their structure-activity (structure-toxicity) relationship at electronic level. An examination of frontier orbitals obtained for ground and protonated forms of the compounds revealed that HOMOs and LUMOs were mainly represented by nitrogen atom and benzyl/benzoylester orbitals with -OH and -OCOCH(3) contributions. The results obtained from this research have confirmed the experimental findings suggesting that neurotoxins acting at type 2 receptor site of voltage-dependent sodium channel are activators and blockers with common structural features and differ only in efficacy. The energetic tendency of HOMO-LUMO energy gap can probably distinguish activators and blockers that have been observed. Genetic Algorithm with Multiple Linear Regression Analysis (GA-MLRA) technique was also applied for the generation of three-descriptor QSAR models for the set of 65 blockers. Additionally to the computational studies, the HOMO-LUMO gap descriptor in each obtained QSAR model has confirmed the crucial role of charge transfer in receptor-ligand interactions. A number of other descriptors such as logP, I(BEG), nNH2, nHDon, nCO have been selected as complementary ones to LUMO and their role in activity alteration has also been discussed.

journal_name

Comput Biol Chem

journal_title

Computational biology and chemistry

authors

Turabekova MA,Rasulev BF,Levkovich MG,Abdullaev ND,Leszczynski J

doi

10.1016/j.compbiolchem.2007.10.003

subject

Has Abstract

pub_date

2008-04-01 00:00:00

pages

88-101

issue

2

eissn

1476-9271

issn

1476-928X

pii

S1476-9271(07)00143-0

journal_volume

32

pub_type

杂志文章

相关文献

COMPUTATIONAL BIOLOGY AND CHEMISTRY文献大全
  • Cryptic tRNAs in chaetognath mitochondrial genomes.

    abstract：:The chaetognaths constitute a small and enigmatic phylum of little marine invertebrates. Both nuclear and mitochondrial genomes have numerous originalities, some phylum-specific. Until recently, their mitogenomes seemed containing only one tRNA gene (trnMet), but a recent study found in two chaetognath mitogenomes two...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.04.007

    authors： Barthélémy RM,Seligmann H

    更新日期：2016-06-01 00:00:00

  • A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model.

    abstract：:The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world,...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107192

    authors： Hattori LT,Gutoski M,Vargas Benítez CM,Nunes LF,Lopes HS

    更新日期：2020-02-01 00:00:00

  • Understand the acquired resistance of RTK inhibitors by computational receptor tyrosine kinases network.

    abstract：:Receptor Tyrosine Kinase inhibitors are the most popular anti-cancer drug types. But the resistance is the major challenge. Our study on the network with 1334 proteins and their 2623 interactions which retrieved from 52 RTKs indicated that most RTKs proteins were the key controllers of the protein-protein network. Dir...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.07.017

    authors： Tian Y,Ma Y,Wu S,Zhang T,Li Z,Wang G,Zhang J

    更新日期：2018-10-01 00:00:00

  • Prediction of novel pluripotent proteins involved in reprogramming of male Germline stem cells (GSCs) into multipotent adult Germline stem cells (maGSCs) by network analysis.

    abstract：:Germline stem cells (GSCs) are known to transmit genetic information from parents to offspring. These GSCs can undergo reprogramming to transform themselves into pluripotent stem cells, called as Multipotent adult Germline stem cells (maGSCs). The mechanism of the reprogramming of GSCs to maGSCs is elusive. To investi...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.08.001

    authors： Guttula PK,Agarwal A,Maharana U,Gupta MK

    更新日期：2018-10-01 00:00:00

  • Exploiting the performance of dictionary-based bio-entity name recognition in biomedical literature.

    abstract：:Bio-entity name recognition is the key step for information extraction from biomedical literature. This paper presents a dictionary-based bio-entity name recognition approach. The approach expands the bio-entity name dictionary via the Abbreviation Definitions identifying algorithm, improves the recall rate through th...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2008.03.008

    authors： Yang Z,Lin H,Li Y

    更新日期：2008-08-01 00:00:00

  • A deep learning ensemble for function prediction of hypothetical proteins from pathogenic bacterial species.

    abstract：:Protein function prediction is a crucial task in the post-genomics era due to their diverse irreplaceable roles in a biological system. Traditional methods involved cost-intensive and time-consuming molecular biology techniques but they proved to be ineffective after the outburst of sequencing data through the advent ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107147

    authors： Mishra S,Rastogi YP,Jabin S,Kaur P,Amir M,Khatun S

    更新日期：2019-12-01 00:00:00

  • Computational insight into the phthalocyanine-DNA binding via docking and molecular dynamics simulations.

    abstract：:Phthalocyanines are considered as good DNA binders, which makes them promising anti-tumor drug leads. The purpose of this study is to investigate the interactions between DNA and quaternary metallophthalocyanine derivatives (Q-MPc) possessing varying metals (M = Zn, Ni, Cu, Fe, Mg and Ca) by molecular docking since th...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.09.009

    authors： Ozalp L,Sağ Erdem S,Yüce-Dursun B,Mutlu Ö,Özbil M

    更新日期：2018-12-01 00:00:00

  • Determining common insertion sites based on retroviral insertion distribution across tumors.

    abstract：:A CIS (common insertion site) indicates a genome region that is hit more frequently by retroviral insertions than expected by chance. Such a region is strongly related to cancer gene loci, which leads to the detection of cancer genes. An algorithm for detecting CISs should satisfy the following: (1) it does not requir...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2014.03.001

    authors： Chen F,Li Z,Chen YP

    更新日期：2014-08-01 00:00:00

  • In silico allergenicity prediction of several lipid transfer proteins.

    abstract：:Non-specific lipid transfer proteins (nsLTPs) are common allergens and they are particularly widespread within the plant kingdom. They have a highly conserved three-dimensional structure that generate a strong cross-reactivity among the members of this family. In the last years several web tools for the prediction of ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2015.11.006

    authors： Garino C,Coïsson JD,Arlorio M

    更新日期：2016-02-01 00:00:00

  • Computational identification of novel microRNA homologs in the chimpanzee genome.

    abstract：:MicroRNAs are important negative regulators of gene expression in higher eukaryotes. The miRNA repertoire of the closest human animal relative, the chimpanzee (Pan troglodytes), is largely unknown. In this study, we focused on computational search of novel miRNA homologs in chimpanzee. We have searched and analyzed th...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2008.07.024

    authors： Baev V,Daskalova E,Minkov I

    更新日期：2009-02-01 00:00:00

  • Patterns of cation binding to the aromatic amino acid R groups in Trp, Tyr, and Phe.

    abstract：:Previous joint experimental and theoretical work demonstrates that typically soluble peptides will be rendered insoluble in the presence of saturated sodium ions in aqueous solution due to disruption of cation-π interactions between Trp and Lys. The present work utilizes quantum chemical methods including density func...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2017.12.009

    authors： Scherer SL,Stewart AL,Fortenberry RC

    更新日期：2018-02-01 00:00:00

  • Spectroscopic, quantum computational and molecular docking studies on 1-phenylcyclopentane carboxylic acid.

    abstract：:The vibrational wavenumbers of optimized molecular structure of 1-phenylcyclopentane carboxylic acid (1PCPCA) molecule have been calculated by quantum chemical theory and compared with experimental results. The density functional theory (DFT) approach is followed using the method B3LYP and 6-311++G(d,p) basis set. Usi...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.05.011

    authors： Raajaraman BR,Sheela NR,Muthu S

    更新日期：2019-10-01 00:00:00

  • Potential protein biomarkers for systemic lupus erythematosus determined by bioinformatics analysis.

    abstract：:Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disorder, and its pathogenesis in males and in cases without accompanying lupus nephritis (LN-) is not fully understood. In this study, we identified 90 (82 up- and 8 downregulated) differentially expressed genes (DEGs) common to female LN-, female LN+ a...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.107135

    authors： Kong J,Li L,Zhimin L,Yan J,Ji D,Chen Y,Yuanyuan W,Chen X,Shao H,Wang J,Da Z

    更新日期：2019-12-01 00:00:00

  • New insights on gene regulation in archaea.

    abstract：:Archaea represent an important and vast domain of life. This cellular domain includes a large diversity of organisms characterized as prokaryotes with basal transcriptional machinery similar to eukarya. In this work we explore the most recent findings concerning the transcriptional regulatory organization in archaeal ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章,评审

    doi：10.1016/j.compbiolchem.2011.10.006

    authors： Tenorio-Salgado S,Huerta-Saquero A,Perez-Rueda E

    更新日期：2011-12-14 00:00:00

  • MODULEWRITER: a program for automatic generation of database interfaces.

    abstract：:MODULEWRITER is a PERL object relational mapping (ORM) tool that automatically generates database specific application programming interfaces (APIs) for SQL databases. The APIs consist of a package of modules providing access to each table row and column. Methods for retrieving, updating and saving entries are provide...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/s1476-9271(03)00021-5

    authors： Zheng CL,Fana F,Udupi PV,Gribskov M

    更新日期：2003-05-01 00:00:00

  • Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study.

    abstract：:Human Leukocyte Antigens (HLA) are highly polymorphic proteins that play a key role in the immune system. HLA molecule is present on the cell membrane of antigen-presenting cells of the immune system and presents short peptides, originating from the proteins of invading pathogens or self-proteins, to the T-cell Recept...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.02.019

    authors： Ozbek P

    更新日期：2016-06-01 00:00:00

  • Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin.

    abstract：:Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from ri...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107245

    authors： Hussain A,Shahbaz M,Tariq M,Ibrahim M,Hong X,Naeem F,Khalid Z,Raza HMZ,Bo Z,Bin L

    更新日期：2020-06-01 00:00:00

  • Phosphorylation mapping of laminin α1-chain: Kinases in association with active sites.

    abstract：:Laminin-111 is a trimeric glycoprotein of the extracellular matrix (ECM) that holds a significant role in cell adhesion, migration and differentiation. Laminin-111 is the most studied laminin isoform, composed of three chains; α1, β1 and γ1. Phosphorylation is the most common eukaryotic post - translational modificati...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2019.04.012

    authors： Galliou PA,Verrou KM,Koliakos G

    更新日期：2019-06-01 00:00:00

  • In silico structural and functional analysis of Mesorhizobium ACC deaminase.

    abstract：:Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of bioti...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2017.02.005

    authors： Pramanik K,Soren T,Mitra S,Maiti TK

    更新日期：2017-06-01 00:00:00

  • Putative dual inhibitors of Janus kinase 1 and 3 (JAK1/3): Pharmacophore based hierarchical virtual screening.

    abstract：:Janus kinase 1 and 3 are non-receptor protein tyrosine kinases, involved in the regulation of various cytokines implicated in the pathogenesis of autoimmune and inflammatory disease conditions. Thus, they serve as therapeutic targets for the designing of multi-targeted agents for the treatment of inflammatory-mediated...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.07.009

    authors： Jasuja H,Chadha N,Singh PK,Kaur M,Bahia MS,Silakari O

    更新日期：2018-10-01 00:00:00

  • Prioritization of potential drug targets against P. aeruginosa by core proteomic analysis using computational subtractive genomics and Protein-Protein interaction network.

    abstract：:Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide. It is involved in nosocomial infections. In the current study, potential novel drug targets against P. aeruginosa have been identified using core prot...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.02.017

    authors： Uddin R,Jamil F

    更新日期：2018-06-01 00:00:00

  • QSAR classification-based virtual screening followed by molecular docking studies for identification of potential inhibitors of 5-lipoxygenase.

    abstract：:Developments of novel inhibitors to prevent the function of 5-lipoxygenase (5-LOX) proteins that are responsible for a variety of inflammatory and allergic disease are a major challenge in the scientific community. In this study, robust QSAR classification models for predicting 5-LOX activity were developed using mach...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2018.10.002

    authors： Shameera Ahamed TK,Rajan VK,Sabira K,Muraleedharan K

    更新日期：2018-12-01 00:00:00

  • Chemical reaction optimization for solving shortest common supersequence problem.

    abstract：:Shortest common supersequence (SCS) is a classical NP-hard problem, where a string to be constructed that is the supersequence of a given string set. The SCS problem has an enormous application of data compression, query optimization in the database and different bioinformatics activities. Due to NP-hardness, the exac...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2016.05.004

    authors： Khaled Saifullah CM,Rafiqul Islam M

    更新日期：2016-10-01 00:00:00

  • Analysis of compensatory substitution and gene evolution on the MAGEA/CSAG-palindrome of the primate X chromosomes.

    abstract：:The human X chromosome contains a large number of inverted repeat DNA palindromes. Although arbitrary substitutions destroyed the inverted repeat structure of MAGEA/CSAG-palindrome during the evolutionary process of the primates, most of the substitutions are compensatory. Using maximum parsimony, it is demonstrated t...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2012.11.002

    authors： Qi Y,Lu H,Ai D

    更新日期：2013-02-01 00:00:00

  • Prognostic prediction of carcinoma by a differential-regulatory-network-embedded deep neural network.

    abstract：:The accurate prognostic prediction is essential for precise diagnosis and treatment of carcinoma. In addition to clinical survival prediction method, many computational methods based on transcriptomic data have been proposed to build the prediction models and study the prognosis of cancer patients. We propose a differ...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107317

    authors： Li J,Ping Y,Li H,Li H,Liu Y,Liu B,Wang Y

    更新日期：2020-10-01 00:00:00

  • DNA strand break: structural and electrostatic properties studied by molecular dynamics simulation.

    abstract：:Due to their lethal consequences and a relatively high probability of introduction of repair errors and mutations, single and double strand breaks are among the most important and dangerous DNA lesions. However, the mechanisms of their recognition and repair processes are only poorly known at present. This work define...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2005.12.001

    authors： Bunta JK,Laaksonen A,Pinak M,Nemoto T

    更新日期：2006-04-01 00:00:00

  • Protein function prediction using neighbor relativity in protein-protein interaction network.

    abstract：:There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interact...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2012.12.003

    authors： Moosavi S,Rahgozar M,Rahimi A

    更新日期：2013-04-01 00:00:00

  • Protein kinase inhibitors' classification using K-Nearest neighbor algorithm.

    abstract：:Protein kinases are enzymes acting as a source of phosphate through ATP to regulate protein biological activities by phosphorylating groups of specific amino acids. For that reason, inhibiting protein kinases with an active small molecule plays a significant role in cancer treatment. To achieve this aim, computational...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107269

    authors： Arian R,Hariri A,Mehridehnavi A,Fassihi A,Ghasemi F

    更新日期：2020-06-01 00:00:00

  • Discovery of potential inhibitor against human acetylcholinesterase: a molecular docking and molecular dynamics investigation.

    abstract：:Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2017.04.002

    authors： Singh SP,Gupta D

    更新日期：2017-06-01 00:00:00

  • Study of the structure and binding site features of FaEXPA2, an α-expansin protein involved in strawberry fruit softening.

    abstract：:Tissue softening accompanies the ripening of many fruits and initiates the processes of irreversible deterioration. Expansins are plant cell wall proteins that have been proposed to disrupt hydrogen bonds within the cell wall polymer matrix. Several authors have shown that FaEXPA2 is a key gene that shows an increased...

    journal_title：Computational biology and chemistry

    pub_type： 杂志文章

    doi：10.1016/j.compbiolchem.2020.107279

    authors： Valenzuela-Riffo F,Morales-Quintana L

    更新日期：2020-05-30 00:00:00