scholarly journals Docking-Based 3D-QSAR Studies for 1,3,4-oxadiazol-2-one Derivatives as FAAH Inhibitors

2021 ◽  
Vol 22 (11) ◽  
pp. 6108
Author(s):  
Agata Zięba ◽  
Tuomo Laitinen ◽  
Jayendra Z. Patel ◽  
Antti Poso ◽  
Agnieszka A. Kaczor
Keyword(s):  
Hydrogen Bond ◽  
Statistical Significance ◽  
External Validation ◽  
3D Qsar ◽  
Field Calculation ◽  
Hydrogen Bond Donor ◽  
Statistical Parameters ◽  
Comfa Model ◽  
Donor And Acceptor ◽  
Faah Inhibitors

This work aimed to construct 3D-QSAR CoMFA and CoMSIA models for a series of 31 FAAH inhibitors, containing the 1,3,4-oxadiazol-2-one moiety. The obtained models were characterized by good statistical parameters: CoMFA Q2 = 0.61, R2 = 0.98; CoMSIA Q2 = 0.64, R2 = 0.93. The CoMFA model field contributions were 54.1% and 45.9% for steric and electrostatic fields, respectively. In the CoMSIA model, electrostatic, steric, hydrogen bond donor, and hydrogen acceptor properties were equal to 34.6%, 23.9%, 23.4%, and 18.0%, respectively. These models were validated by applying the leave-one-out technique, the seven-element test set (CoMFA r2test-set = 0.91; CoMSIA r2test-set = 0.91), a progressive scrambling test, and external validation criteria developed by Golbraikh and Tropsha (CoMFA r20 = 0.98, k = 0.95; CoMSIA r20 = 0.98, k = 0.89). As the statistical significance of the obtained model was confirmed, the results of the CoMFA and CoMSIA field calculation were mapped onto the enzyme binding site. It gave us the opportunity to discuss the structure–activity relationship based on the ligand–enzyme interactions. In particular, examination of the electrostatic properties of the established CoMFA model revealed fields that correspond to the regions where electropositive substituents are not desired, e.g., in the neighborhood of the 1,3,4-oxadiazol-2-one moiety. This highlights the importance of heterocycle, a highly electronegative moiety in this area of each ligand. Examination of hydrogen bond donor and acceptor properties contour maps revealed several spots where the implementation of another hydrogen-bond-donating moiety will positively impact molecules’ binding affinity, e.g., in the neighborhood of the 1,3,4-oxadiazol-2-one ring. On the other hand, there is a large isopleth that refers to the favorable H-bond properties close to the terminal phenoxy group of a ligand, which means that, generally speaking, H-bond acceptors are desired in this area.

scholarly journals Molecular Modeling Studies of Substituted 2,4,5-Trisubstituted Triazolinones Aryl and Nonaryl Derivatives as Angiotensin II AT1Receptor Antagonists

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Mukesh C. Sharma ◽  
D. V. Kohli ◽  
Smita Sharma
Keyword(s):  
Simulated Annealing ◽  
Statistical Significance ◽  
External Validation ◽  
Feature Selection Method ◽  
3D Qsar ◽  
Field Analysis ◽  
Molecular Field ◽  
Hydrogen Bond Donor ◽  
Molecular Field Analysis ◽  
Qsar Models

The development of new therapies to treat hypertension and cardiovascular diseases. A series of 2,4,5-trisubstituted triazolinones aryl and nonaryl derivatives were subjected toGroup-based QSAR,k-nearest neighbourmolecular field analysis, and pharmacophore mapping. Multiple linear regression (MLR) methodology coupled with feature selection method namely simulated annealing, was applied to derive Group based QSAR models which were further validated for statistical significance and predictive ability by internal and external validation. The best physicochemical descriptors, namely, R1chiV1, R2T_N_O_3, R2chlorines count, R2T_C_N_4, and R2SssNHE index, contribute significantly to the biological activity. The statistically significant best Group-based QSAR model hasr2=0.8357andq2=0.7266with pred_r2=0.8138. The 3D-QSAR studies were performed using the simulated annealing selectionk-nearest neighbormolecular field analysis approach; a leave-one-out cross-validated correlation coefficientq2=0.7461and predicate activity pred_r2=0.7790were obtained. Contour maps using this approach showed that steric, electrostatic, and hydrophobic effects dominantly determine binding affinities. Pharmacophore hypotheses were generated by the mol sign module and found to contain common features like hydrogen bond donor acceptor, donor, positive, negative ionizable, and hydrophobic features. This model can be used for preliminary screening of large number of substituted 3H-1,-2,-4 triazolinone aryl and nonaryl derivatives. The information rendered by 3D-QSAR models may lead to a better understanding of structural requirements of triazolinone aryl and nonaryl derivatives and also aid in designing novel potent antihypertensive molecules.

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.

The hydrogen bond donor and acceptor ability of thioformic acid

2011 ◽  
Vol 22 (5) ◽  
pp. 1015-1030 ◽  
Author(s):  
Damanjit Kaur ◽  
Ritika Sharma ◽  
Darpandeep Aulakh
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor

Synthesis and preliminary bioactivity evaluation of new pregnane brassinosteroid-like compounds

2005 ◽  
Vol 83 (8) ◽  
pp. 1084-1092 ◽  
Author(s):  
Daniel G Rivera ◽  
Francisco Coll
Keyword(s):  
Hydrogen Bond ◽  
Plant Growth ◽  
Hypocotyl Elongation ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor ◽  
Plant Growth Promoting ◽  
Plant Growth Promoting Activity ◽  
Growth Promoting ◽  
Cotyledon Expansion

Seven new pregnane compounds bearing some representative A- and B-ring brassinosteroid functions, as well as hydrogen bond donor and acceptor ones on the D ring, were efficiently synthesized. The obtained compounds did not show remarkable plant growth-promoting activity in the radish hypocotyl elongation and cotyledon expansion bioassays, however, introducing oxygen and amino functions on the D ring led to an enhancement of the bioactivity. The 16β-functionalized pregnane brassinosteroid-like compounds were slightly more active than the 16α-functionalized ones.Key words: steroids, brassinosteroids, pregnane analogues.

Identification of new checkpoint kinase-1 (Chk1) inhibitors by docking, 3D-QSAR, and pharmacophore-modeling methods

2012 ◽  
Vol 90 (8) ◽  
pp. 675-692 ◽  
Author(s):  
Premlata K. Ambre ◽  
Raghuvir R. S. Pissurlenkar ◽  
Evans C. Coutinho ◽  
Radhakrishnan P. Iyer
Keyword(s):  
Hydrogen Bond ◽  
3D Qsar ◽  
Pharmacophore Modeling ◽  
Docking Studies ◽  
Hydrogen Bond Donor ◽  
Hydrogen Bond Acceptor ◽  
Checkpoint Kinase ◽  
Checkpoint Kinase 1 ◽  
Qsar Models ◽  
Potential Inhibitors

Inhibition of checkpoint kinase-1 (Chk1) by small molecules is of great therapeutic interest in the field of oncology and for understanding cell-cycle regulations. This paper presents a model with elements from docking, pharmacophore mapping, the 3D-QSAR approaches CoMFA, CoMSIA and CoRIA, and virtual screening to identify novel hits against Chk1. Docking, 3D-QSAR (CoRIA, CoMFA and CoMSIA), and pharmacophore studies delineate crucial site points on the Chk1 inhibitors, which can be modified to improve activity. The docking analysis showed residues in the proximity of the ligands that are involved in ligand–receptor interactions, whereas CoRIA models were able to derive the magnitude of these interactions that impact the activity. The ligand-based 3D-QSAR methods (CoMFA and CoMSIA) highlight key areas on the molecules that are beneficial and (or) detrimental for activity. The docking studies and 3D-QSAR models are in excellent agreement in terms of binding-site interactions. The pharmacophore hypotheses validated using sensitivity, selectivity, and specificity parameters is a four-point model, characterized by a hydrogen-bond acceptor (A), hydrogen-bond donor (D), and two hydrophobes (H). This map was used to screen a database of 2.7 million druglike compounds, which were pruned to a small set of potential inhibitors by CoRIA, CoMFA, and CoMSIA models with predicted activity in the range of 8.5–10.5 log units.

C–H⋯S interaction exhibits all the characteristics of conventional hydrogen bonds

2020 ◽  
Vol 22 (31) ◽  
pp. 17482-17493 ◽  
Author(s):  
Sanat Ghosh ◽  
Pragya Chopra ◽  
Sanjay Wategaonkar
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Hydrogen Bond Donor ◽  
Donor And Acceptor

This is a tale of a pair of a hydrogen bond donor and acceptor, namely the CH donor and sulphur acceptor, neither of which is a conventional hydrogen bond participant.

New polymorphs of an old drug: conformational and synthon polymorphism of 5-nitrofurazone

2016 ◽  
Vol 72 (2) ◽  
pp. 263-273 ◽  
Author(s):  
Dorota Pogoda ◽  
Jan Janczak ◽  
Veneta Videnova-Adrabinska
Keyword(s):  
Hydrogen Bond ◽  
Molecular Conformation ◽  
Crystal Packing ◽  
Molecular Organization ◽  
Hydrogen Bond Donor ◽  
Scanning Calorimetry ◽  
Geometrical Isomers ◽  
Crystal Forms ◽  
Donor And Acceptor ◽  
Polymorphic Forms

Two new polymorphic forms of 5-nitrofurazone (5-nitro-2-furaldehyde semicarbazone) have been synthesized and structurally characterized by single-crystal and powder X-ray diffraction methods, vibrational spectroscopy (FT–IR and temperature Raman), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and Hirshfeld surface analysis. The compound crystallizes in three different polymorphic formsP21/a(polymorph α),P21(polymorph β) andP21/c(polymorph γ), the crystal structures of two of which (polymorphs β and γ) represent new structure determinations. The solid-state molecular organization in the three crystal forms is analyzed and discussed in terms of molecular conformation, crystal packing and hydrogen-bonded networks. All three crystals are formed fromtransgeometrical isomers, but the molecular conformation of the α-polymorph issyn–anti–anti–anti, while that of β- and γ-polymorphs issyn–anti–syn–syn. As a consequence of this the hydrogen-bond donor and acceptor sites of the molecules are oriented differently, which in turn results in different hydrogen-bond connectivity and packing patterns.

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