Homogeneous assay for zearalenone analogues and their docking studies with apo-/holo-estrogen receptors

2019 ◽  
Vol 11 (2) ◽  
pp. 192-199 ◽  
Author(s):  
Jie Zhang ◽  
Wenfu Wu ◽  
Yifan Song ◽  
Ligang Hou ◽  
Tiezhu Li ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Estrogen Receptors ◽  
Docking Studies ◽  
Structural Basis ◽  
Homogeneous Assay

A homogeneous assay was developed for zearalenone analogues and the structural basis of their estrogenicity was demonstrated by molecular docking.

scholarly journals Structural analysis of rice Os4BGlu18 monolignol β-glucosidase

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0241325
Author(s):  
Supaporn Baiya ◽  
Salila Pengthaisong ◽  
Sunan Kitjaruwankul ◽  
James R. Ketudat Cairns
Keyword(s):  
Molecular Docking ◽  
Substrate Specificity ◽  
Disulfide Bonds ◽  
Complex Structure ◽  
Docking Studies ◽  
Structural Basis ◽  
Glycoside Hydrolase Family ◽  
Multiple Sequence ◽  
X Ray Crystallography ◽  
Tim Barrel

Monolignol glucosides are storage forms of monolignols, which are polymerized to lignin to strengthen plant cell walls. The conversion of monolignol glucosides to monolignols is catalyzed by monolignol β-glucosidases. Rice Os4BGlu18 β-glucosidase catalyzes hydrolysis of the monolignol glucosides, coniferin, syringin, and p-coumaryl alcohol glucoside more efficiently than other natural substrates. To understand more clearly the basis for substrate specificity of a monolignol β-glucosidase, the structure of Os4BGlu18 was determined by X-ray crystallography. Crystals of Os4BGlu18 and its complex with δ-gluconolactone diffracted to 1.7 and 2.1 Å resolution, respectively. Two protein molecules were found in the asymmetric unit of the P212121 space group of their isomorphous crystals. The Os4BGlu18 structure exhibited the typical (β/α)8 TIM barrel of glycoside hydrolase family 1 (GH1), but the four variable loops and two disulfide bonds appeared significantly different from other known structures of GH1 β-glucosidases. Molecular docking studies of the Os4BGlu18 structure with monolignol substrate ligands placed the glycone in a similar position to the δ-gluconolactone in the complex structure and revealed the interactions between protein and ligands. Molecular docking, multiple sequence alignment, and homology modeling identified amino acid residues at the aglycone-binding site involved in substrate specificity for monolignol β-glucosides. Thus, the structural basis of substrate recognition and hydrolysis by monolignol β-glucosidases was elucidated.

scholarly journals Identification of APOE4 modulators, targeted therapeutic candidates in Coronary Artery Disease, using Molecular Docking studies

2021 ◽  
Author(s):  
Lima Hazarika ◽  
Supriyo Sen ◽  
Akshaykumar Zawar ◽  
Jitesh Doshi
Keyword(s):  
Coronary Artery Disease ◽  
Molecular Docking ◽  
Coronary Artery ◽  
Binding Affinity ◽  
Intramolecular Interaction ◽  
Docking Studies ◽  
Structural Basis ◽  
Molecular Docking Studies ◽  
Artery Disease ◽  
Drug Receptor

AbstractA significant genetic suspect for coronary artery disease is the pathological adaptation of apolipoprotein E4 (APOE4) through intramolecular interaction. With the prevailing evidences on APOE4 genotype and its prevalence in coronary artery disease, the present study has investigated the protein–ligand binding affinity and unveil the receptor binding abilities of different classes of ligands for APOE4 through molecular docking studies. Structural basis of APOE4 involvement in CAD suggests that the intramolecular domain interactions to be a suitable target for therapeutic intervention. Various classes of ligands including known drugs used in the treatment of CAD, fragment-based stabilizers and their similar structures and molecules with known bioactivity against APOE4 were screened for their binding affinity and further investigated for their interactions with APOE4. Computational studies show the benzyl amide derived structures to be useful candidates in modulation of APOE4. The dynamics of the binding analysis can be further achieved with an in-depth understanding of drug-receptor interactions performing molecular dynamic simulation studies.

scholarly journals Estrogenic Effect of Scoparia dulcis (Linn) Extract in Mice Uterus and In Silico Molecular Docking Studies of Certain Compounds with Human Estrogen Receptors

2020 ◽  
Author(s):  
Khamhee Wangsa ◽  
Indira Sarma ◽  
Purbajyoti Saikia ◽  
Dhanabalan Ananthakrishnan ◽  
Hirendra Nath Sarma ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Estrogen Receptors ◽  
Binding Affinity ◽  
In Silico ◽  
Md Simulations ◽  
Docking Studies ◽  
Female Reproduction ◽  
Molecular Docking Studies ◽  
Scoparia Dulcis ◽  
In Silico Molecular Docking

Background: Scoparia dulcis Linn. is reported to be used by women of Assam and Arunachal Pradesh in northeast India for treating menstrual disorders. Scoparia dulcis contains compounds that bind with estrogen receptors (ERα and ERβ) evidenced by increased PCNA in endometrial epithelium. Methods: Crude extract was orally administered at the dose of 500 mg/kg body weight/day to the female mice (60–70 days old) in five different groups. Each group containing six females included: (I) cyclic control, (II) cyclic extract treated, (III) Ovariectomized (OVX)-vehicle treated (Control), (IV) OVX-E2 treated (V) OVX- extract treated. Extract was administered for eight days to the cyclic groups and three days to the OVX groups. PCNA was detected immunohistochemically in uterine tiss ues and signals were analyzed by Image J software (NIH, USA). Compounds were separated by GC-MS and identified using NIST. In silico molecular docking studies was performed with human estrogen receptors (ERα and ERβ). Molecular dynamics (MD) simulations of the best interacting compound was done using gromacs. Results: The results showed cell proliferation in the uterine endometrium evidenced by PCNA. Two phytocompounds, Octadecanoic acid and methyl stearate showed binding affinity with ERα and ERβ. Conclusion: Scoparia dulcis contains compounds having binding affinity with ERα and ERβ. The present study is the first report on compounds from Scoparia dulcis showing binding affinity with human estrogen receptors which may have biological effect on female reproduction.

The Interaction of Isoflavone Phytoestrogens with ERα and ERβ by Molecular Docking and Molecular Dynamics Simulations

2020 ◽  
Vol 16 ◽  
Author(s):  
Ting Wang ◽  
Yaquan Liu ◽  
Xuming Zhuang ◽  
Feng Luan ◽  
Chunyan Zhao
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Docking ◽  
Estrogen Receptors ◽  
Molecular Dynamics Simulations ◽  
Binding Free Energy ◽  
Docking Studies ◽  
The Body ◽  
Factors Affecting ◽  
Dynamics Simulations

Aim and Objective: Isoflavone phytoestrogens, which commonly present in natural plants, are closely related to human health. The combination of them with estrogen receptors in the body can play a more important role in the prevention and treatment of cardiovascular diseases, cancer, and menopausal diseases. This research is conducted for the wider application of isoflavone phytoestrogens in various fields. Method: In this study, molecular docking studies and molecular dynamics simulations were performed to explore the affinities and interaction between three typical isoflavone phytoestrogens and estrogen receptors (ERα and ERβ), respectively. Results and Conclusion: Molecular docking results showed that the affinity of genistein, daidzein and formononetin was different, and the ligand structures and hydrogen bonds force were the main factors affecting the binding abilities. The calculation of the binding free energy shows the stability of the complex and the contribution of various interactions to the binding free energy. The decomposition of binding free energy indicates that van der Waals interaction and electrostatic interaction promote the binding of the complex, which are in agreement with the docking studies.

scholarly journals Structural analysis of rice Os4BGlu18 monolignol β-glucosidase

2020 ◽  
Author(s):  
Supaporn Baiya ◽  
Salila Pengthaisong ◽  
James R. Ketudat Cairns
Keyword(s):  
Molecular Docking ◽  
Substrate Specificity ◽  
Disulfide Bonds ◽  
Complex Structure ◽  
Docking Studies ◽  
Structural Basis ◽  
Glycoside Hydrolase Family ◽  
Multiple Sequence ◽  
X Ray Crystallography ◽  
Tim Barrel

AbstractMonolignol glucosides are storage forms of monolignols, which are polymerized to lignin to strengthen plant cell walls. The conversion of monolignol glucosides to monolignols is catalyzed by monolignol β-glucosidases. Rice Os4BGlu18 β-glucosidase catalyzes hydrolysis of the monolignol glucosides, coniferin, syringin, and p-coumaryl alcohol glucoside more efficiently than other natural substrates. To understand more clearly the basis for substrate specificity of a monolignol β-glucosidase, the structure of Os4BGlu18 was determined by X-ray crystallography. Crystals of Os4BGlu18 and its complex with δ-gluconolactone diffracted to 1.7 and 2.1 Å resolution, respectively. Two protein molecules were found in the asymmetric unit of the P212121 space group of their isomorphous crystals. The Os4BGlu18 structure exhibited the typical (β/α)8 TIM barrel of glycoside hydrolase family 1 (GH1), but the four variable loops and two disulfide bonds appeared significantly different from other known structures of GH1 β-glucosidases. Molecular docking studies of the Os4BGlu18 structure with monolignol substrate ligands placed the glycone in a similar position to the δ-gluconolactone in the complex structure and revealed the interactions between protein and ligands. Molecular docking, multiple sequence alignment, and homology modeling identified amino acid residues at the aglycone-binding site involved in substrate specificity for monolignol β-glucosides. Thus, the structural basis of substrate recognition and hydrolysis by monolignol β-glucosidases was elucidated.

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