Retrospective molecular docking study of WY-25105 ligand to β-secretase and bias of the three-dimensional structure flexibility

2013 ◽  
Vol 19 (8) ◽  
pp. 2971-2979 ◽  
Author(s):  
Leo Ghemtio ◽  
Nicolas Muzet
Keyword(s):  
Molecular Docking ◽  
Three Dimensional ◽  
Docking Study ◽  
Dimensional Structure ◽  
Molecular Docking Study ◽  
Three Dimensional Structure ◽  
Structure Flexibility

scholarly journals SOLATION, CHARACTERIZATION, AND DOCKING STUDIES OF ISOLATED COMPOUNDS AS ANTIDIABETIC MOLECULES FROM CRESSA CRETICA

2020 ◽  
pp. 84-91
Author(s):  
SANGEETA RANI ◽  
KAVITA GAHLOT ◽  
ARVIND KUMAR
Keyword(s):  
Molecular Docking ◽  
Spectroscopic Analysis ◽  
Three Dimensional ◽  
Data Bank ◽  
Docking Study ◽  
Docking Studies ◽  
Dimensional Structure ◽  
Lead Target ◽  
Coarse Powder ◽  
Autodock 4.0

Objective: The purpose of this study was to investigate the diabetic effect of phytocompounds isolated from Cressa cretica Linn. using spectroscopic analysis and molecular docking studies. Methods: Coarse powder of the whole plant of C. cretica was extracted with methanol, extracted part was subjected to silica column isolation, and two compounds: 2-Isopropyl-4-(1-methyl-dodeca-2,4-dienyloxy)-benzene-1,3,5-triol (Compound CN-01) and 11-Methyl-dodeca-2,4,6,8,10-pentenoic acid 2,3-dihydroxy-5-methyl-phenyl ester (Compound CN-02) were isolated in pure form. The three-dimensional structure of target protein was downloaded from PDB (www.rcsb.org) Protein Data Bank, Ligand file CN – 01 and CN – 02 were converted to MDL Molfile (V2000) format using ChemSketch 2017.2.1. These files could not be used directly in AutoDock 4.0 tools; thus, they were first converted to PDB files using an open babel tool. Results: Compounds were revealed through spectroscopic analysis and screened using AutoDock 4.0 tools. Docking study recommended that CN – 01 and CN – 02 an existing phytochemical from the plant of C. cretica had the highest fitness docking score and hence could be a potent antidiabetic drug. Conclusion: In this investigation, we docked the receptor (glycogen phosphorylase protein) holds a promising lead target formation against diabetes based on molecular docking analysis (minimum hydrogen bond length and maximum docked score). Thus, these compounds can be effectively used as drugs for treating diabetes which is predicted on the basis of docking scores.

scholarly journals STUDI MOLECULAR DOCKING SENYAWA GOLONGAN FLAVONOL SEBAGAI ANTIBAKTERI

2018 ◽  
Vol 1 (2) ◽  
pp. 20-27
Author(s):  
Isna Wardaniati ◽  
Muhammad Azhari Herli
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
In Silico ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Receptor Interactions

In this paper we studied the bioactive compounds of Flavonol-D-alanil D-alanin dekarboksipeptidase receptor interactions In silico. First, prepared three dimensional structure of D-alanil D-alanin dekarboksipeptidase as receptor. Preparation of fourth bioactive compounds of flavonol which will be as ligands, klokasilin and D-alanil D-alanin as a comparison. The fourth bioactive compounds of flavonol, klokasilin and D-alanil D-alanin were docked with D-alanil D-alanin dekarboksipeptidase until energy values were obtained. The fourth bioactive compounds of flavonol had lesser binding energy values than D-alanil D-alanin, Quercitrine and rutin also predicted to have greater binding energy and binding affinity than klokasilin (antibiotic) and D-alanil D-alanin (nature ligand).

scholarly journals A Review on Molecular Docking

2021 ◽  
pp. 60-68
Author(s):  
Khemnar Manisha Dnyandev ◽  
Galave Vishal Babasaheb ◽  
Kulkarni Vaishali Chandrashekhar ◽  
Menkudale Amruta Chandrakant ◽  
Otari Kishor Vasant
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Molecular Biology ◽  
Drug Design ◽  
Three Dimensional ◽  
Important Application ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Essential Components ◽  
Structural Databases

Molecular docking is computational modeling of structure complexes formed by two or more interacting molecule. The goal of molecular docking is prediction of three dimensional structure of interest. Molecular docking software mostly used in drug improvement. Molecules and effortless entrance to structural databases has befallen essential mechanism. Molecular Docking provide a collection of expensive tools for drug design and analysis. Simple prophecy of molecules and easy way in to structural databases has become essential components on the desktop of the medicinal chemist. The most important application of molecular docking is virtual screening. A variety of docking programs were residential to imagine the three dimensional structure of the molecule and docking gain can also be analyze with the assist of dissimilar computational methods. Molecular docking is a key tool in structural molecular biology and computer-assist drug design. Docking can be worn to execute virtual screening on large libraries of compounds, rank the results, and suggest structural hypotheses of how the ligands reduce the target, which is precious in lead optimization.

scholarly journals Identification of the occurrence and potential mechanisms of heterotopic ossification associated with 17-beta-estradiol targeting MKX by bioinformatics analysis and cellular experiments

PeerJ ◽  
2022 ◽  
Vol 9 ◽  
pp. e12696
Author(s):  
Yunpeng Zhang ◽  
Jingwei Zhang ◽  
Chenyu Sun ◽  
Fan Wu
Keyword(s):  
Molecular Docking ◽  
Heterotopic Ossification ◽  
Bioinformatics Analysis ◽  
Three Dimensional ◽  
Enrichment Analysis ◽  
Dimensional Structure ◽  
Pathway Enrichment Analysis ◽  
Surgical Trauma ◽  
Three Dimensional Structure ◽  
Histone Deacetylase 1

Background Tendon heterotopic ossification (HO) is a common condition occurring secondary to tendon injury or surgical trauma that significantly affects the patient’s quality of life. The treatment of tendon HO remains challenging due to a lack of clarity regarding the pathological mechanism. Mohawk (MKX) is a key factor in preventing tendon HO; however, its upstream regulatory mechanism remains to be understood. This study aimed to identify potential compounds that target and regulate MKX and explore their functional mechanisms. Methods Bioinformatics analysis of MKX-related compounds and proteins was performed based on data from the STITCH and OncoBinder databases. Subsequently, the SymMap database was used to study MKX-related traditional Chinese medicine drugs and symptoms. Next, the OncoBinder genomic and proteomic discovery model was applied to identify potential regulators of MKX. The analytical tool Expert Protein Analysis System for proteomics was used to predict the three-dimensional structure of MKX, and the AutoDockTools software was used to identify pockets of activity at potential sites for molecular docking. Furthermore, we evaluated the effect of different doses of 17-beta-estradiol on bone marrow-derived mesenchymal stem cells (BM-MSCs). Results By predicting the three-dimensional structure of MKX and simulating molecular docking, Pro-Tyr and 17-beta-Estradiol were found to target and bind to MKX. Analysis of the STITCH and OncoBinder databases showed that MKX had a significant regulatory correlation with suppressor interacting 3 A/histone deacetylase 1 (SIN3A/HDAC1). The GO and KEGG pathway enrichment analysis revealed that the functions of MKX and its associated proteins were mainly enriched in osteogenic-related pathways. Assessment of the proliferation of BM-MSCs revealed that 17-beta-estradiol possibly upregulated the mRNA expression of the HDAC1-SIN3A/BMP pathway-related RUNX2, thereby promoting the proliferation of BM-MSCs. Conclusions The compounds Pro-Tyr and 17-beta-Estradiol may bind to MKX and thus affect the interaction of MKX with SIN3A/HDAC1.

scholarly journals Molecular docking study of potential phytochemicals and their effects on the complex of SARS-CoV2 spike protein and human ACE2

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Anamika Basu ◽  
Anasua Sarkar ◽  
Ujjwal Maulik
Keyword(s):  
Natural Products ◽  
Molecular Docking ◽  
Antiviral Activity ◽  
Binding Sites ◽  
Transmembrane Protein ◽  
Experimental Studies ◽  
Docking Study ◽  
Spike Protein ◽  
Dimensional Structure ◽  
Molecular Docking Study

Abstract Angiotensin converting enzyme 2 (ACE2) (EC:3.4.17.23) is a transmembrane protein which is considered as a receptor for spike protein binding of novel coronavirus (SARS-CoV2). Since no specific medication is available to treat COVID-19, designing of new drug is important and essential. In this regard, in silico method plays an important role, as it is rapid and cost effective compared to the trial and error methods using experimental studies. Natural products are safe and easily available to treat coronavirus affected patients, in the present alarming situation. In this paper five phytochemicals, which belong to flavonoid and anthraquinone subclass, have been selected as small molecules in molecular docking study of spike protein of SARS-CoV2 with its human receptor ACE2 molecule. Their molecular binding sites on spike protein bound structure with its receptor have been analyzed. From this analysis, hesperidin, emodin and chrysin are selected as competent natural products from both Indian and Chinese medicinal plants, to treat COVID-19. Among them, the phytochemical hesperidin can bind with ACE2 protein and bound structure of ACE2 protein and spike protein of SARS-CoV2 noncompetitively. The binding sites of ACE2 protein for spike protein and hesperidin, are located in different parts of ACE2 protein. Ligand spike protein causes conformational change in three-dimensional structure of protein ACE2, which is confirmed by molecular docking and molecular dynamics studies. This compound modulates the binding energy of bound structure of ACE2 and spike protein. This result indicates that due to presence of hesperidin, the bound structure of ACE2 and spike protein fragment becomes unstable. As a result, this natural product can impart antiviral activity in SARS CoV2 infection. The antiviral activity of these five natural compounds are further experimentally validated with QSAR study.

Homology Modeling of Aeromonas hydrophila Laccase and its Molecular Docking with the 2,5-Xylidine

2013 ◽  
Vol 798-799 ◽  
pp. 83-86
Author(s):  
Dong Xia Du ◽  
Shi Ping Shan ◽  
De Yuan Zhang ◽  
Yue Lin He
Keyword(s):  
Molecular Docking ◽  
Homology Modeling ◽  
Aeromonas Hydrophila ◽  
Three Dimensional ◽  
Industrial Effluents ◽  
Binding Pocket ◽  
Binding Mode ◽  
Major Effect ◽  
Dimensional Structure ◽  
Three Dimensional Structure

Laccases belonging to multicopper oxidase family oxidize a broad range of reducing substrates, especially industrial effluents-derived polyphenols, which causing major effect on human health as well as environment. In order to investigate the molecular mechanism of interaction between laccase and its substrate, it is a good idea to analyze three-dimensional structure of laccase. Based on crystal structure ofEscherichia colilaccase CueO, the three-dimensional structure ofAeromonas hydrophilaLaccase (Ah-lac) was constructed by homology modeling and further evaluated using PROSA energy and ERRAT. The substrate binding site in Ah-lac was predicted and the binding mode of 2,5-Xylidine as a putative ligand to Ah-lac was presented using molecular docking. The residues of Met378 and His382 in the binding pocket are responsible for the interactions with 2,5-Xylidine via two hydrogen bonds. The two residues could be important for substrate recognition.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

Three-Dimensional Structure of Cloned T3 Connector Protein at 1.6nm Resolution

1990 ◽  
Vol 48 (1) ◽  
pp. 282-283
Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa
Keyword(s):  
Dna Sequences ◽  
Expression Vector ◽  
Three Dimensional ◽  
Deae Cellulose ◽  
Dna Packaging ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Freezing And Thawing ◽  
Three Dimensional Structure ◽  
Dimensional Reconstruction

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.

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