scholarly journals Interaction of Irbesartan with Bovine Hemoglobin Using Spectroscopic Techniques and Molecular Docking

2012 ◽  
Vol 27 ◽  
pp. 119-128 ◽  
Author(s):  
Ai-Ping Yang ◽  
Mei-Hua Ma ◽  
Xiao-Hua Li ◽  
Mao-Yun Xue
Keyword(s):  
Hydrogen Bond ◽  
Molecular Docking ◽  
Binding Site ◽  
Binding Free Energy ◽  
Protein Secondary Structure ◽  
Cd Spectroscopy ◽  
Electrostatic Energy ◽  
Bovine Hemoglobin ◽  
Spectroscopic Techniques ◽  
Hydrogen Bond Formation

The binding of irbesartan to bovine hemoglobin (BHb) has been investigated for the first time by using UV-Vis absorption, fluorescence, circular dichroism (CD), and molecular docking. The binding site numbernand binding constantKwere calculated to be 1 and , respectively. The alternations of protein secondary structure in the presence of irbesartan was demonstrated using CD spectroscopy. Furthermore, molecular docking indicated that irbesartan could bind to the site 2 of BHb. The analysis of the binding site of irbesartan within the BHb molecule suggested that hydrophobic interaction, hydrogen bond formation, and electrostatic interaction could account for the binding of irbesartan. The hydrogen bond of irbesartan with His87 in the C chain of BHb has been formed. The electrostatic energy, van der Waals energy, and binding free energy were calculated to be −460.3, −224.2, and−684.5 kcal, respectively.

scholarly journals The interaction of clenbuterol hydrochloride with bovine hemoglobin using spectroscopic techniques and molecular modeling methods

2009 ◽  
Vol 23 (5-6) ◽  
pp. 271-279 ◽  
Author(s):  
Yun Wu ◽  
Hui Mao ◽  
Bo Zhao ◽  
Jian Shen
Keyword(s):  
Molecular Modeling ◽  
Protein Secondary Structure ◽  
Binding Mode ◽  
Bovine Hemoglobin ◽  
Spectroscopic Techniques ◽  
Electronic Interaction ◽  
Physiological Conditions ◽  
Modeling Methods ◽  
Clenbuterol Hydrochloride ◽  
Hoff Equation

The interaction of clenbuterol hydrochloride (CL) to bovine hemoglobin (BHb) under physiological conditions was investigated by using UV-vis absorption, fluorescence, circular dichroism (CD) and molecular modeling. The fluorescence intensity of BHb decreased regularly with the gradual increasing concentration of CL. It is observed that there was a prominent interaction between CL and BHb. The fluorescence data revealed that the fluorescence quenching is a static process, and the thermodynamic parameters were calculated according to the Van't Hoff equation. The alternations of protein secondary structure in the presence of CL were determined by the evidence of CD. Molecular modeling study that corroborate our experimental results revealed that the binding mode of CL–BHb complex could be attributed to the hydrophobic interaction and hydrogen bonding, but electronic interaction cannot be excluded.

scholarly journals Synthesis, characterization (IR, 1H, 13C & 31P NMR), fungicidal, herbicidal and molecular docking evaluation of steroid phosphorus compounds

2019 ◽  
Vol 17 (1) ◽  
pp. 621-628 ◽  
Author(s):  
Mahboob Alam ◽  
Youngwon Kim ◽  
Soonheum Park
Keyword(s):  
Molecular Docking ◽  
Binding Free Energy ◽  
Docking Study ◽  
Herbicidal Activity ◽  
Phosphorus Compounds ◽  
Moderate Activity ◽  
Spectroscopic Techniques ◽  
Molecular Docking Study ◽  
Mycelium Growth ◽  
Phosphorus Containing

AbstractPhosphorus containing steroidal derivatives such as 3β-oxo-[diazaphosphalidine-2’-one] stigmast-5-ene and 3β-oxo-[diazaphosphalidine-2’-one] stigmast-5,22-diene were designed, synthesized and characterized using spectroscopic techniques (IR, 1H, 13C & 31P NMR, HRMS) and elemental analysis. The fungicidal and herbicidal studies of the compounds were performed and the experimental outcomes showed that compound 4 showed a good fungicidal activity against mycelium growth of fungi, while in the case of herbicidal activity, both compounds show a moderate activity compared to the commercial drug; Atrazine. The binding free energy of active compound 4 to the receptor named 4-Hydroxyphenylpyruvate dioxygenase (HPPD) was calculated using the molecular docking study. The HPPD is one of the most effective targets of plants for the herbicide study.

Solvent effects on the tautomeric equilibrium of 2,4-pentanedione

1982 ◽  
Vol 60 (10) ◽  
pp. 1178-1182 ◽  
Author(s):  
J. N. Spencer ◽  
Eric S. Holmboe ◽  
Mindy R. Kirshenbaum ◽  
Daniel W. Firth ◽  
Patricia B. Pinto
Keyword(s):  
Hydrogen Bond ◽  
Solvent Effects ◽  
Tautomeric Equilibrium ◽  
Spectroscopic Techniques ◽  
Hydrogen Bond Formation ◽  
Entropy Changes ◽  
Tautomeric Forms ◽  
Self Association ◽  
Enol Tautomer ◽  
Intramolecular Hydrogen

The influence of solvent on the equilibrium position of the tautomeric forms of 2,4-pentanedione was studied by calorimetric and nmr spectroscopic techniques. For solvents such as CCl4 and cyclohexane the intramolecular bond of the enol form persists and bulk solvent effects account for the equilibrium enol–keto content. In solvents such as DMSO, disruption of the intramolecular bond occurs and the percentage of enol falls due to unfavorable entropy changes. The enol intramolecular bond is disrupted by the solvents water and methanol. Enol hydrogen bond formation through self-association and with the solvent accounts for the entropy changes upon enolization in these solvents. The thermodynamic parameters for enolization in neat 2,4-pentanedione are rationalized by the disruption of the enol intramolecular hydrogen bond through consequent polymerization of the enol tautomer.

Interaction of Human Alpha-2-Macroglobulin with Pesticide Aldicarb Using Spectroscopy and Molecular Docking

2020 ◽  
Vol 27 ◽  
Author(s):  
Swati Dixit ◽  
Mohammad Khalid Zia ◽  
Tooba Siddiqui ◽  
Haseeb Ahsan ◽  
Fahim Halim Khan
Keyword(s):  
Molecular Docking ◽  
Receptor Binding ◽  
Crop Production ◽  
Potato Crop ◽  
Cd Spectroscopy ◽  
Docking Studies ◽  
Binding Domain ◽  
Spectroscopic Techniques ◽  
Receptor Binding Domain ◽  
Other Substances

Background: Aldicarb is a carbamate pesticide commercially used in potato crop production. Once it enters human body, it interacts with diverse proteins and other substances. Objective: Aldicarb is toxic to human health and it is also a cholinesterase inhibitor, which prevents the breakdown of acetylcholine in synapse. Human alpha-2-macroglobulin (α2M), is a large tetrameric glycoprotein of 720 kDa with antiproteinase activity, found abundantly in plasma. Methods: In the present study, the interaction of aldicarb with alpha-2-macroglobulin was explored utilizing various spectroscopic techniques and molecular docking studies. Results: UV-vis and fluorescence spectroscopy suggests the formation of a complex between aldicarb and α2M apparent by increased absorbance and decreased fluorescence with static quenching mode. CD spectroscopy indicates a slight change in the structure of alpha-2-macroglobulin. Docking studies confirm the interaction of aldicarb with Pro- 1391, Leu-1392, Lys1393, Val-1396, Lys- 1397, Thr-1408, Glu-1409, Val-1410, Asp-282 and Glu-281 in the receptor binding domain at the Cterminal of the alpha 2 macroglobulin. Discussion: In this work, aldicarb is shown to bind with alpha 2-macroglobulin at receptor binding domain which is the binding site for various extracellular and intracellular ligand too. Also, affecting the functional activity of the protein may lead to further physiological consequences. Conclusion: It is possible that aldicarb binds and compromises antiproteinase activity of α2M and binding properties by inducing changes in the secondary structure of the protein.

scholarly journals Structure-Based Virtual Screening and Molecular Dynamic Simulation Studies to Identify Novel Cytochrome bc1 Inhibitors as Antimalarial Agents

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Rahul P. Gangwal ◽  
Gaurao V. Dhoke ◽  
Mangesh V. Damre ◽  
Kanchan Khandelwal ◽  
Abhay T. Sangamwar
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Molecular Dynamic Simulation ◽  
Molecular Dynamic ◽  
Dynamic Simulation ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Van Der Waals Interactions ◽  
Electrostatic Energy ◽  
Hydrogen Bond Acceptor

Cytochrome bc1 (EC 1.10.2.2, bc1) is an essential component of the cellular respiratory chain, which catalyzes electron transfer from quinol to cytochrome c and concomitantly the translocation of protons across the membrane. It has been identified as a promising target in malaria parasites. The structure-based pharmacophore modelling and molecular dynamic simulation approach have been employed to identify novel inhibitors of cytochrome bc1. The best structure-based pharmacophore hypothesis (Hypo1) consists of one hydrogen bond acceptor (HBA), one general hydrophobic (HY), and two hydrophobic aromatic features (HYAr). Further, hydrogen interactions and hydrophobic interactions of known potent inhibitors with cytochrome bc1 were compared with Hypo1, which showed that the Hypo1 has good predictive ability. The validated Hypo1 was used to screen the chemical databases. The hits obtained were subsequently subjected to the molecular docking analysis to identify false-positive hits. Moreover, the molecular docking results were further validated by molecular dynamics simulations. Binding-free energy analysis using MM-GBSA method reveals that the van der Waals interactions and the electrostatic energy provide the basis for favorable absolute free energy of the complex. The five virtual hits were identified as possible candidates for the designing of potent cytochrome bc1 inhibitors.

scholarly journals Effects of Baicalein and Chrysin on the Structure and Functional Properties of β-Lactoglobulin

Foods ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 165
Author(s):  
Ang Li ◽  
Lei Chen ◽  
Weijie Zhou ◽  
Junhui Pan ◽  
Deming Gong ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Molecular Docking ◽  
Functional Properties ◽  
Sulfhydryl Group ◽  
Surface Hydrophobicity ◽  
Dynamics Simulation ◽  
Foaming Properties ◽  
Hydrogen Bond Formation ◽  
Simulation Techniques ◽  
Β Lactoglobulin

Two flavonoids with similar structures, baicalein (Bai) and chrysin (Chr), were selected to investigate the interactions with β-lactoglobulin (BLG) and the influences on the structure and functional properties of BLG by multispectral methods combined with molecular docking and dynamic (MD) simulation techniques. The results of fluorescence quenching suggested that both Bai and Chr interacted with BLG to form complexes with the binding constant of the magnitude of 105 L·mol−1. The binding affinity between BLG and Bai was stronger than that of Chr due to more hydrogen bond formation in Bai–BLG binding. The existence of Bai or Chr induced a looser conformation of BLG, but Chr had a greater effect on the secondary structure of BLG. The surface hydrophobicity and free sulfhydryl group content of BLG lessened due to the presence of the two flavonoids. Molecular docking was performed at the binding site of Bai or Chr located in the surface of BLG, and hydrophobic interaction and hydrogen bond actuated the formation of the Bai/Chr–BLG complex. Molecular dynamics simulation verified that the combination of Chr and BLG decreased the stability of BLG, while Bai had little effect on it. Moreover, the foaming properties of BLG got better in the presence of the two flavonoids compounds and Bai improved its emulsification stability of the protein, but Chr had the opposite effect. This work provides a new idea for the development of novel dietary supplements using functional proteins as flavonoid delivery vectors.

scholarly journals Interaction of thiacloprid with bovine hemoglobin using spectroscopic and molecular modeling methods

2010 ◽  
Vol 24 (5) ◽  
pp. 559-566
Author(s):  
Chang-Yun Chen ◽  
Bo Zhao ◽  
Zheng-Wu Wang
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Modeling ◽  
Protein Secondary Structure ◽  
Binding Constants ◽  
Entropy Change ◽  
Binding Mode ◽  
Cd Spectroscopy ◽  
Bovine Hemoglobin ◽  
Standard Entropy ◽  
Α Helix

The interaction of thiacloprid (TL) to bovine hemoglobin (BHb) under physiological conditions was investigated by using fluorescence spectroscopy, circular dichroism spectroscopy (CD) and molecular modeling. The fluorescence intensity of BHb decreased regularly with the gradual increasing concentration of TL. It is observed that there was a prominent interaction between TL and BHb. The binding constantsKAat 288, 298 and 308 K obtained are 8.04, 5.26 and 3.08×104l · mol–1, respectively. The standard enthalpy change (ΔH°) and the standard entropy change (ΔS°) are calculated to be –34.54 KJ · mol–1and –25.77 J · mol–1 · K–1, which indicated that hydrogen bonding forces play major role in the interaction between TL and BHb. The alternations of protein secondary structure in the presence of TL were determined by CD spectroscopy. The results revealed that the content of α-helix was decreased from 51.85% in free BHb to 48.14% in TL–BHb complex. Molecular modeling study and our experimental results both showed that the binding mode of TL–BHb complex could be attributed to hydrogen bonding and hydrophobic interaction.

scholarly journals Structural Requirements of N-alpha-Mercaptoacetyl Dipeptide (NAMdP) Inhibitors of Pseudomonas Aeruginosa Virulence Factor LasB: 3D-QSAR, Molecular Docking, and Interaction Fingerprint Studies

2019 ◽  
Vol 20 (24) ◽  
pp. 6133 ◽  
Author(s):  
José Luis Velázquez-Libera ◽  
Juliana Andrea Murillo-López ◽  
Alexander F. de la Torre ◽  
Julio Caballero
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Hydrogen Bond ◽  
Molecular Docking ◽  
Binding Site ◽  
Virulence Factor ◽  
External Validation ◽  
3D Qsar ◽  
Interaction Patterns ◽  
Ligand Interaction ◽  
Hydrogen Bond Acceptor

The zinc metallopeptidase Pseudomonas elastase (LasB) is a virulence factor of Pseudomonas aeruginosa (P. aeruginosa), a pathogenic bacterium that can cause nosocomial infections. The present study relates the structural analysis of 118 N-alpha-mercaptoacetyl dipeptides (NAMdPs) as LasB inhibitors. Field-based 3D-QSAR and molecular docking methods were employed to describe the essential interactions between NAMdPs and LasB binding sites, and the chemical features that determine their differential activities. We report a predictive 3D-QSAR model that was developed according to the internal and external validation tests. The best model, including steric, electrostatic, hydrogen bond donor, hydrogen bond acceptor, and hydrophobic fields, was found to depict a three-dimensional map with the local positive and negative effects of these chemotypes on the LasB inhibitory activities. Furthermore, molecular docking experiments yielded bioactive conformations of NAMdPs inside the LasB binding site. The series of NAMdPs adopted a similar orientation with respect to phosphoramidon within the LasB binding site (crystallographic reference), where the backbone atoms of NAMdPs are hydrogen-bonded to the LasB residues N112, A113, and R198, similarly to phosphoramidon. Our study also included a deep description of the residues involved in the protein–ligand interaction patterns for the whole set of NAMdPs, through the use of interaction fingerprints (IFPs).

scholarly journals Molecular docking studies of 1, 3, 4 oxadiazoles Derivatives as anti-convulsive agents

2020 ◽  
Vol 8 (1) ◽  
pp. 151-179
Author(s):  
Sachin Jangra ◽  
Sachin Kumar ◽  
Manjusha Choudhary
Keyword(s):  
Amino Acids ◽  
Hydrogen Bond ◽  
Molecular Docking ◽  
Binding Site ◽  
Gabaa Receptor ◽  
Small Molecule ◽  
Future Research ◽  
Computational Technique ◽  
Standard Drug ◽  
Hydrogen Bond Interactions

Molecular docking is a computational technique that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and estimates its binding affinity. The present study attempted the high throughput in-silico screening of 65 compounds docked with the GABAA receptor (PDB ID: 4COF) using Molegro virtual docker (6.0). Out of these 65 compounds, 17 compounds showed very good mol dock score in ranging between -66.344 & -102.653. Ethosuximide and Carbamazepine drugs was used as a standard drug which showed mol dock score -50.6357 & -58.5047 respectively. Most of test compounds demonstrated excellent number of hydrogen bond interactions viz compounds 33, 38, 39, 45, 47, 53, 54, 59, 61, 62, 63, 64 & 65 which showed 7 to 11 number of hydrogen bond interactions as compared to standard drug interactions values 6 & 5 respectively and also showed the interaction with same amino acids Glu52, Ser51and Val53 and some other amino acids Asn54, Thr58 and Thr133 also showed very acceptable bond length less than 3.91Å. The obtained results indicated that all studied ligands have similar position and orientation inside the putative binding site of GABAA receptor (PDB ID: 4COF) which reveals a large space bounded by a membrane-binding domain which serves as an entry channel for substrate to the active site. In addition, the affinity of any small molecule can be considered as a unique tool in the field of drug design and offer prospective in future research to develop a potent anticonvulsant agent.

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