scholarly journals Biological Activity of Selected Compounds from Annona muricata Seed as Antibreast Cancer Agents: Theoretical Study

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Abel Kolawole Oyebamiji ◽  
Gideon Femi Tolufashe ◽  
Olubukola Monisola Oyawoye ◽  
Temitope A. Oyedepo ◽  
Banjo Semire
Keyword(s):  
Hydrogen Bond ◽  
Anticancer Activity ◽  
Simulation Method ◽  
Docking Study ◽  
Log P ◽  
Annona Muricata ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Discovery Studio ◽  
Compound C

Several natural products have been of help to humans, and its effect is noticeable in the medicinal world. Soursop with botanical name Annona muricata L. possesses antidiarrhea, anticold fever, antirheumatism, and antineuralgia properties. In this work, five selected molecular compounds were studied against type 3 of 3α-hydroxysteroid dehydrogenase (3α-HSD). Its anticancer activity was investigated using the quantum chemical method via Spartan 14 software, molecular docking via Discovery studio 2017, AutoDock Tool 1.5.6, AutoDock Vina 1.1.2, and PyMol 1.7.4.4 and the molecular dynamic simulation method via AMBER14 molecular dynamics package. Many descriptors (EHOMO, ELUMO, dipole moment, energy bandgap, area, volume, polarizability, polar surface area, Log P, hydrogen bond donor, and hydrogen bond acceptor) which describe the anticancer activity of the studied compounds were obtained. Also, the docking study revealed the inhibiting ability of the studied compound, and it was observed that compound C possesses a greater ability to inhibit than other studied compounds as well as the standard (5FU).

6,9-Dibromo-2a,10b-diphenyl-2a,5,10,10b-tetrahydro-2H,3H-2,3,4a,10a-tetraazabenzo[g]cyclopenta[cd]azulene-1,4-dione monohydrate

2006 ◽  
Vol 62 (5) ◽  
pp. o1754-o1755
Author(s):  
Neng-Fang She ◽  
Sheng-Li Hu ◽  
Hui-Zhen Guo ◽  
An-Xin Wu
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Supramolecular Structure ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Compound C ◽  
Bifurcated Hydrogen Bond

The title compound, C24H18Br2N4O2·H2O, forms a supramolecular structure via N—H...O, O—H...O and C—H...O hydrogen bonds. In the crystal structure, the water molecule serves as a bifurcated hydrogen-bond acceptor and as a hydrogen-bond donor.

Identification of Selective Receptor Modulators Using Pharmacoinformatics Approaches for Therapeutic Application in Estrogen Therapy

2019 ◽  
Vol 4 (2) ◽  
pp. 52-81
Author(s):  
Md Ataul Islam ◽  
Shovonlal Bhowmick ◽  
Achintya Saha
Keyword(s):  
Hydrogen Bond ◽  
Estrogen Therapy ◽  
Docking Study ◽  
Hydrogen Bond Donor ◽  
Molecular Docking Study ◽  
Hydrogen Bond Acceptor ◽  
Validation Tests ◽  
Receptor Modulators ◽  
Analysis Of Binding Energy ◽  
Pharmacophore Models

Pharmacoinformatics strategies have been applied to explore promising selective estrogen receptor (ER) modulators (SERMs). A set of non-steroidal ligands was considered for both ERα and ERβ subtypes. Best pharmacophore models revealed with importance of hydrogen bond acceptor and hydrophobicity for both subtypes, along with an aromatic ring and hydrogen bond donor for α and β subtypes, respectively. Both models were validated, and further considered for virtual screening of National Cancer Institute database. Initial hits were sorted with a number of criteria, and finally the molecules have been proposed as promising SERMs. A molecular docking study explained that screened ligands formed a number of binding interactions with both ERs. The subtype receptors in complex with active and screened compounds were considered for molecular simulations to compare stability of the complexes. An analysis of binding energy found that screened ligands hold a strong affinity towards the selective receptor cavity. The proposed ligands might be promising leads for estrogen therapy after experimental validation tests.

Pharmacophore-based screening for identification of Human Acyl-CoA cholesterol acyltransferase inhibitors: An in-silico study

2020 ◽  
Vol 18 ◽  
Author(s):  
Ankit Dhaundiyal ◽  
Puja Kumari ◽  
Shasta Kalra
Keyword(s):  
Hydrogen Bond ◽  
Cholesterol Acyltransferase ◽  
Three Dimensional ◽  
Pharmacophore Model ◽  
Fatty Acyl ◽  
Hydrogen Bond Donor ◽  
Data Set ◽  
Hydrogen Bond Acceptor ◽  
Discovery Studio ◽  
Acyltransferase Inhibitors

Abstract:: Human Acyl-CoA cholesterol acyltransferase (ACAT) plays an important role in catalysis of reaction which converts cholesterol into cholesteryl esters and long-chain fatty acyl coenzyme A. The inhibition of ACAT has therapeutically potential roles in hypercholestrolemia, atherosclerosis and coronary heart disease. For better understanding of essential chemical features for ACAT inhibition and identifying novel inhibitors, a three-dimensional (3D) chemical-feature-based quantitative QSAR pharmacophore model for available ACAT inhibitors have been developed for first time using Discovery Studio 2.5. The best model (Hypo1) having lowest total cost (84.14), highest cost difference (69.67), highest correlation coefficient (0.94), and lowest RMS (1.15Å), constitutes of one hydrogen bond acceptor, one hydrogen bond donor, two hydrophobic aromatic and one hydrophobic aliphatic feature. Validation of Hypo1 was further done using test set activity prediction, Fischer’s randomization method and decoy data set to check the reliability of the model. The validated Hypo1 was then used as a 3D search query for virtual screening to retrieve potential inhibitors from National cancer institute (NCI), ChemDiv and Specs databases. Finally, ADMET properties of selected compounds were calculated. The result shows the good potential of the newly found ACAT inhibitors. Finally, the two compounds have been obtained as novel hits to design the Novel ACAT inhibitors.

scholarly journals Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Christoph A. Bauer ◽  
Gisbert Schneider ◽  
Andreas H. Göller
Keyword(s):  
Machine Learning ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Training Data ◽  
Free Energies ◽  
Hydrogen Bond Donor ◽  
Chemical Application ◽  
Hydrogen Bond Acceptor ◽  
Donor And Acceptor ◽  
Target Values

Abstract We present machine learning (ML) models for hydrogen bond acceptor (HBA) and hydrogen bond donor (HBD) strengths. Quantum chemical (QC) free energies in solution for 1:1 hydrogen-bonded complex formation to the reference molecules 4-fluorophenol and acetone serve as our target values. Our acceptor and donor databases are the largest on record with 4426 and 1036 data points, respectively. After scanning over radial atomic descriptors and ML methods, our final trained HBA and HBD ML models achieve RMSEs of 3.8 kJ mol−1 (acceptors), and 2.3 kJ mol−1 (donors) on experimental test sets, respectively. This performance is comparable with previous models that are trained on experimental hydrogen bonding free energies, indicating that molecular QC data can serve as substitute for experiment. The potential ramifications thereof could lead to a full replacement of wetlab chemistry for HBA/HBD strength determination by QC. As a possible chemical application of our ML models, we highlight our predicted HBA and HBD strengths as possible descriptors in two case studies on trends in intramolecular hydrogen bonding.

scholarly journals The Characteristics of PD-L1 Inhibitors, from Peptides to Small Molecules

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1940 ◽  
Author(s):  
Yanwen Zhong ◽  
Xuanyi Li ◽  
Hequan Yao ◽  
Kejiang Lin
Keyword(s):  
Hydrogen Bond ◽  
Small Molecules ◽  
Pharmacophore Model ◽  
Amino Acid Residues ◽  
Tumor Treatment ◽  
Hydrogen Bond Donor ◽  
Treatment Results ◽  
Hydrogen Bond Acceptor ◽  
Checkpoint Pathway ◽  
Pharmacophore Models

The programmed cell death ligand protein 1 (PD-L1) is a member of the B7 protein family and consists of 290 amino acid residues. The blockade of the PD-1/PD-L1 immune checkpoint pathway is effective in tumor treatment. Results: Two pharmacophore models were generated based on peptides and small molecules. Hypo 1A consists of one hydrogen bond donor, one hydrogen bond acceptor, two hydrophobic points and one aromatic ring point. Hypo 1B consists of one hydrogen bond donor, three hydrophobic points and one positive ionizable point. Conclusions: The pharmacophore model consisting of a hydrogen bond donor, hydrophobic points and a positive ionizable point may be helpful for designing small-molecule inhibitors targeting PD-L1.

Moxifloxacin/Gatifloxacin‐1,2,3‐triazole‐isatin Hybrids with Hydrogen‐Bond Donor and Their In Vitro Anticancer Activity

2019 ◽  
Vol 56 (9) ◽  
pp. 2691-2694 ◽  
Author(s):  
Rongxing Chen ◽  
Hao Zhang ◽  
Tianwei Ma ◽  
Huarui Xue ◽  
Zhong Miao ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Anticancer Activity ◽  
Hydrogen Bond Donor

Hydrogen-bond thio acceptors in O-methyl 3,4-dimethylpyrrole-2-thiocarboxylate

2007 ◽  
Vol 63 (11) ◽  
pp. o4217-o4217 ◽  
Author(s):  
Tobias Kerscher ◽  
Peter Klüfers ◽  
Wolfgang Kügel
Keyword(s):  
Hydrogen Bond ◽  
Title Compound ◽  
Van Der Waals ◽  
Hydrogen Bond Acceptor ◽  
Molecular Plane ◽  
Bond Lengths ◽  
Dimer Structure ◽  
Compound C ◽  
Oxo Compounds ◽  
Centrosymmetric Dimers

Molecules of the title compound, C8H11NOS, are flat and almost C s-symmetric. Bond lengths and angles resemble calculated values at the B3LYP/6-311+G(2 d,p) level of theory. The solid is characterized by van der Waals bonding and π stacking (stacking distance = 3.352 Å) of the basic motif of the structure: planar centrosymmetric dimers that are bonded by pairs of symmetry-equivalent N—H...S bonds. The dimer structure is rationalized by the nature of the hydrogen-bond acceptor orbital, the S(3p) orbital located in the molecular plane. The double-donor–double-acceptor situation in the dimer results in an unusual C=S...H angle of about 127° which is large compared with isolated C=S...H bonds (circa 100°), but small compared with the almost linear acceptor geometry in related oxo compounds.

Infrared spectroscopic characterization of hydrogen-bonded propylene oxide − ethanol and propylene oxide − 2-fluoroethanol complexes isolated in solid neon matrices

2013 ◽  
Vol 91 (12) ◽  
pp. 1292-1302 ◽  
Author(s):  
Osama Y. Ali ◽  
Elyse Jewer ◽  
Travis D. Fridgen
Keyword(s):  
Hydrogen Bond ◽  
Propylene Oxide ◽  
Spectroscopic Characterization ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Reduced Frequency ◽  
Enthalpy Of Proton Transfer ◽  
The Difference ◽  
Bonded Complexes ◽  
Hydrogen Bonded

The infrared absorption spectra of hydrogen-bonded complexes of propylene oxide with either ethanol or 2-fluoroethanol have been recorded in neon matrices. Mixtures of propylene oxide and ethanol or propylene oxide and 2-fluoroethanol vapors were mixed with an excess of neon gas and deposited onto a KBr substrate at 4.2 K. The results indicate that hydrogen-bonded complexes were formed with propylene oxide as the hydrogen bond acceptor and either ethanol or 2-fluoroethanol as the hydrogen bond donors. The features assigned to the O−H stretch were red-shifted by 175 and 193 cm−1 for the ethanol- and 2-fluoroethanol-containing complexes, respectively. The difference in red shifts can be accounted for due to the greater acidity of 2-fluroethanol. Deuterium isotope experiments were conducted to help confirm the assignment of the O–H stretch for the complexes. As well, structures and infrared spectra were calculated using B3LYP/6-311++G(2d,2p) calculations and were used to compare with the experimental spectra. A “scaling equation” rather than a scaling factor was used and is shown to greatly increase the utility of the calculations when comparing with experimental spectra. An examination of the O–H stretching red shifts for many hydrogen-bound complexes reveals a relationship between the shift and the difference between the acidity of the hydrogen bond donor and the basicity of the hydrogen bond acceptor (the enthalpy of proton transfer). Both hydrogen-bonded complexes and proton-bound complexes appear to have a maximum in the reduced frequency value that corresponds to complexes where the hydrogen/proton are equally shared between the two bases.

Enthalpies of interaction of nitrogen base solutes with organic solvents

1985 ◽  
Vol 63 (9) ◽  
pp. 2540-2544 ◽  
Author(s):  
W. Kirk Stephenson ◽  
Richard Fuchs
Keyword(s):  
Hydrogen Bond ◽  
Organic Solvents ◽  
Butyl Alcohol ◽  
Hydrogen Bond Donor ◽  
Butyl Ether ◽  
Hydrogen Bond Acceptor ◽  
Nitrogen Base ◽  
Benzene Toluene ◽  
Polar Interactions ◽  
S Model

Heats of solution of triethylamine, aniline, pyridine, and model compounds (3-ethylpentane, benzene) in 17 organic solvents (n-heptane, cyclohexane, carbon tetrachloride, 1,2-dichloroethane, α,α,α-trifluorotoluene, triethylamine, butyl ether, ethyl acetate, dimethylformamide, dimethyl sulfoxide, benzene, toluene, mesitylene, t-butyl alcohol, 1-octanol, methanol, 2,2,2-trifluoroethanol) have been combined with solute heats of vaporization to give enthalpies of transfer from vapor to solvent (ΔH(v → s)). Differences between solute and model values (ΔΔH(v → s) = ΔH(v → s) (solute) – ΔH(v → s) (model)) were used to evaluate nitrogen base solute–solvent polar interactions. Correlations of ΔΔH(v → s) with Taft–Kamlet solvatochromic parameters (π*, α, β) have been determined.Aniline was found to be a better hydrogen bond donor acid than hydrogen bond acceptor base. Nevertheless, alcohols donate H-bonds to aniline. Triethylamine and pyridine are stronger HBA bases than aniline. The π* (dipolarity–polarizability) parameter of aniline (as a solute) is calculated to be 1.10.

SINGLE MOLECULE IMMOBILIZATION OF π-CONJUGATED MOLECULES ON Au USING DENDRIMER-BASED TEMPLATES

2005 ◽  
Vol 04 (04) ◽  
pp. 467-473 ◽  
Author(s):  
ABDELHAK BELAISSAOUI ◽  
HIDEO TOKUHISA ◽  
EMIKO KOYAMA ◽  
MASATOSHI KANESATO
Keyword(s):  
Hydrogen Bond ◽  
Ftir Spectroscopy ◽  
Single Molecule ◽  
Binding Constant ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Interaction ◽  
Hydrogen Bond Acceptor ◽  
Conjugated Molecules ◽  
The Core ◽  
Conjugated Molecule

We demonstrate that immobilization of a π-conjugated molecule containing a bipyridine moiety as a hydrogen bond acceptor on Au using a dendrimer-based template with 3,4-dihydroxybenzene moiety at the core as a hydrogen bond donor. The hydrogen bond interaction was used for the linkage between the conjugated molecule and the template to improve the method to fabricate single-molecule arrays we reported before.1 Although the binding constant is small ( K = 120 ± 20 M -1) in CDCl 3, it was demonstrated that the dendrimer spacer serves as a template to isolate the π-conjugated molecule, and is removable simply with a CH 2 Cl 2 rinsing by surface FTIR spectroscopy.

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