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 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 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.

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.

scholarly journals Molecular Docking and Virtual Screening based prediction of drugs for COVID-19

2020 ◽  
Vol 23 ◽  
Author(s):  
Sekhar Talluri
Keyword(s):  
Clinical Trials ◽  
Molecular Docking ◽  
Virtual Screening ◽  
Genomic Sequence ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Main Protease ◽  
Docking Calculations ◽  
Approved Drugs

Aims: To predict potential drugs for COVID-19 by using molecular docking for virtual screening of drugs approved for other clinical applications. <p> Background: SARS-CoV-2 is the betacoronavirus responsible for the COVID-19 pandemic. It was listed as a potential global health threat by WHO due to high mortality, high basic reproduction number and lack of clinically approved drugs and vaccines for COVID-19. The genomic sequence of the virus responsible for COVID-19, as well as the experimentally determined three dimensional structure of the Main protease are available. <p> </p> Objective: To identify potential drugs that can be repurposed for treatment of COVID-19 by using molecular docking based virtual screening of all approved drugs. <p> </p> Methods: List of drugs approved for clinical use was obtained from SuperDRUG2 database. The structure of the target in the apo form, as well as structures of several target-ligand complexes, were obtained from RCSB PDB. The structure of SARS-CoV-2 Mpro determined from X-ray diffraction data was used as the target. Data regarding drugs in clinical trials for COVID-19 was obtained from clinicaltrials.org. Input for molecular docking based virtual screening was prepared by using Obabel and customized python, bash and awk scripts. Molecular docking calculations were carried out with Vina and SMINA, and the docked conformations were analyzed and visualized with PLIP, Pymol and Rasmol. <p> </p> Results: Among the drugs that are being tested in clinical trials for COVID-19, Danoprevir and Darunavir have the highest binding affinity for the target main protease of SARS-CoV-2. Saquinavir and Beclabuvir were identified as the best novel candidates for COVID-19 therapy by using Virtual Screening of drugs approved for other clinical indications. <p> </p> Conclusion: Protease inhibitors approved for treatment of other viral diseases have the potential to be repurposed for treatment of COVID-19. </p>

scholarly journals Virtual Screening Based Prediction of Potential Drugs for COVID-19

2020 ◽  
Author(s):  
Sekhar Talluri
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Viral Infections ◽  
Genomic Sequence ◽  
Three Dimensional ◽  
Drug Repurposing ◽  
Dimensional Structure ◽  
Main Protease ◽  
Approved Drugs ◽  
Target Effects

SARS-CoV-2 is the betacoronavirus responsible for the COVID-19 pandemic. It was listed as a potential global health threat by WHO due to high mortality, high basic reproduction number and lack of clinically approved drugs and vaccines for COVID-19. The genomic sequence of the virus responsible for COVID-19, as well as the experimentally determined three dimensional structure of the Main protease (Mpro) are available. The reported structure of the target Mpro was utilized in this study to identify potential drugs for COVID-19 using molecular docking based virtual screening of all approved drugs. The results of this study confirm preliminary reports that some of the drugs approved for treatment of other viral infections have the potential for treatment of COVID-19. Selected antiviral drugs, approved for human therapeutic applications, were ranked for potential effectiveness against COVID-19, based on predicted binding energy to the target Mpro of SARS-CoV-2, and novel candidates for drug repurposing were identified in this study. In addition, potential mechanisms for beneficial off target effects of some drugs in clinical trials were identified by using molecular docking.

Review of HIV-1 reverse transcriptase three-dimensional structure: Implications for drug design

1993 ◽  
Vol 1 (1) ◽  
pp. 129-150 ◽  
Author(s):  
Raymond G. Nanni ◽  
Jianping Ding ◽  
Alfredo Jacobo-Molina ◽  
Stephen H. Hughes ◽  
Edward Arnold
Keyword(s):  
Drug Design ◽  
Reverse Transcriptase ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Hiv 1

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.

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